Kenyatta was born into the Kikuyu people in the village of Ngenda, which lay in an area of sugar cane and cattle pasture. His father was named Muigai, and his mother Wambui. They were shamba folk, living in a homestead built on a spur of land near the River Thiririka; they were farmers, raising crops and breeding both sheep and goats. Muigai was sufficiently wealthy that he could afford to keep several wives, each of whom lived in a separate nyom ba (woman's hut). Kenyatta's exact date of birth is not known, as birth records were not traditionally kept by the Kikuyu. It is known that he was probably born sometime in the 1890s. The Kikuyu custom at the time was to divide boys into age groups, in which they would be initiated into manhood together. The older members of Kenyatta's age group are believed to have been born around 1890. One biographer, Jules Archer, suggested that his year of birth was likely 1890, although a fuller analysis performed by Jeremy Murray-Brown concluded that he was likely born circa 1897 or 1898. Kenyatta was raised according to traditional Kikuyu custom and religious belief, and was taught the skills needed to herd the family flock. When he was ten years old, his earlobes were pierced to mark his transition away from childhood.

In November 1909, Kenyatta left home and enrolled as a pupil at the Church of Scotland Mission (CSM) at Thogoto. He informed the British missionaries based there that he wished to learn from them. These missionaries were zealous Christians who believed that bringing Christianity to the indigenous peoples of Eastern Africa was part of Britain's civilising mission. While there, Kenyatta stayed at the small boarding school, where he learnt stories from the Bible, and was taught to read and write in English. He also performed chores for the mission, among them washing the dishes and weeding the gardens. Several months after arriving, Kenyatta was taken ill with tuberculosis. Kenyatta was soon joined at the mission dormitory by his brother Kongo. Many of their generation were increasingly resenting the patronising way in which most of the British missionaries treated them.

Kenyatta's academic progress was unremarkable, and in July 1912 he became an apprentice to the carpenter at the mission. At Easter 1912, he professed his dedication to Christianity and began undergoing catechism. In 1913, he underwent the Kikuyu circumcision ritual; the missionaries generally disapproved of this custom, but it was an important aspect of Kikuyu tradition, allowing Kenyatta to be recognised as an adult. Asked to take a Christian name, he chose both John and Peter after the eponymous Apostles in the New Testament. The missionaries however insisted that he select only one, and so he chose Johnstone, the -stone being selected because it was a Biblical reference to Peter. Accordingly, he was baptised as Johnstone Kamau in August 1914. After his baptism, Kenyatta moved out of the mission dormitory and lived with friends. Having completed his apprenticeship to a carpenter, Kenyatta requested that the mission allow him to be an apprentice stonemason, but they refused. Kenyatta then requested that he be recommended for employment, but the head missionary refused because of an allegation of minor dishonesty.

In 1917, Kenyatta moved to Narok, where he was involved in transporting livestock to Nairobi, possibly as an administrative clerk or a ranching hand. After the British Army conquered German East Africa, Kenyatta relocated to Nairobi where he worked in a store selling farming and engineering equipment. In the evenings, he took classes in a Church Mission School. Several months later he returned to Thika to work with another company, and then gained employment constructing houses for the Thogota Mission. He also lived for a time in Dagoretti, where he became a retainer for a local sub-chief, Kioi; in 1919 he assisted Kioi in putting the latter's case in a land dispute before a Nairobi court.

He has also been described as a talented orator, author, and Editor. Kenyatta had dictatorial and autocratic tendencies, as well as a fierce temper that could emerge as rage on occasion. Murray-Brown noted that Kenyatta could be "quite unscrupulous, even brutal" in using others to get what he wanted, but that he never displayed any physical cruelty or nihilism. Murray-Brown characterised Kenyatta as an "affectionate father" to his children, but one who was frequently absent. Kenyatta had two children from his first marriage with Grace Wahu: son Peter Muigai Kenyatta (born 1920), who later became a deputy minister; and daughter Margaret Kenyatta (born 1928). Margaret served as mayor of Nairobi between 1970 and 1976 and then as Kenya's ambassador to the United Nations from 1976 to 1986. Grace Wahu died in April 2007. His daughter, Wambui Margaret, became his closest confidante. He viewed monogamy through an anthropological lens as an interesting Western phenomenon but did not adopt the practice himself, instead having sexual relations with a wide range of women throughout his life.

Anti-imperialist sentiment was on the rise among both native and Indian communities in Kenya following the success of the Irish War of Independence and the Russian October Revolution. Many indigenous Africans were deeply resentful that they had to carry the kipande identity certificate at all times, were forbidden from growing coffee, and had to pay taxation without political representation. Various political upheavals occurred in Kikuyuland following the end of World War I, among them the campaigns of Harry Thuku and the East African Association which resulted in the government massacre of 21 native protesters in March 1922. Kenyatta had not taken part in any of these events, perhaps so as not to disrupt his lucrative employment prospects. Kenyatta's interest in politics stemmed from his friendship with James Beauttah, a senior figure in the Kikuyu Central Association (KCA). Beauttah took Kenyatta to a political meeting in Pumwani, although this led to no firm involvement at the time. In either 1925 or early 1926, Beauttah moved to Uganda, although remained in contact with Kenyatta. When the KCA wrote to Beauttah and asked him to travel to London as their representative, he declined, but recommended that Kenyatta—who had a good command of the English language—go in his place. Kenyatta accepted, probably on the condition that the Association matched his pre-existing wage. He thus became the group's secretary.

In May 1928, the KCA launched a Kikuyu-language magazine, Muĩgwithania (roughly translated as "The Reconciler" or "The Unifier"), in which it published news, articles, and homilies. Its purpose was to help unify the Kikuyu and to raise funds for the KCA. Kenyatta, now described as Secretary of the KCA, was listed as the publication's Editor, although Murray-Brown suggested that he was not the guiding hand behind it and that his duties were largely confined to translating things into Kikuyu. Kenyatta's approach to campaigning was cautious; he was aware that Thuku had been exiled for his activism. In Muĩgwithania, he expressed support for the churches, district commissioners, and chiefs. He also praised the British Empire, stating that: "The first thing [about the Empire] is that all people are governed justly, big or small – equally. The second thing is that nobody is regarded as a slave, everyone is free to do what he or she likes without being hindered." This did not prevent Grigg from writing to the authorities in London requesting that he be allowed to shut the magazine down.

Kenyatta also developed contacts with radicals to the left of the Labour Party, including several communists. In the summer of 1929, he left London and visited Moscow via Berlin, alleging that the trip had been financed by an African-American friend. He returned to London in October. Kenyatta was strongly influenced by his time in the Soviet Union. Back in England, he wrote three articles on the Kenyan situation for the Communist Party of Great Britain's newspapers, the Daily Worker and Sunday Worker, one published in October and the others in January 1930. In these articles, his criticism of British imperialism was far stronger than it had been in Muĩgwithania. These communist links concerned many of Kenyatta's liberal patrons. In January, Kenyatta met with Drummond Shiels, the undersecretary-of-state, at the House of Commons. Kenyatta told Shiels that he was not affiliated with communist circles and was unaware as to the nature of the newspaper which published his articles. Shiels' advice was for Kenyatta to return home, where he could promote Kikuyu involvement in the constitutional process and discourage violence and extremism. After eighteen months in Europe, Kenyatta had run out of money. The Anti-Slavery Society advanced him funds to pay off his debts and return to Kenya. Although Kenyatta enjoyed life in London and feared arrest if he returned home, he arrived in Mombasa in September 1930. On his return, his prestige among the Kikuyu was high because of his time spent in Europe.

In his absence, the issue of female genital mutilation (FGM) had become a topic of strong debate in Kikuyu society. The Protestant churches, backed by European medics and the colonial authorities, supported the abolition of this traditional practice, but the KCA rallied to its defence, claiming that its abolition would be a threat to the structure and customs of Kikuyu society. Anger between the two sides had heightened, with several churches expelling KCA members from their congregations, and it was widely believed that the January 1930 killing of the American nun, Hulda Stumpf, had been due to the issue. As Secretary of the KCA, Kenyatta soon attended a meeting with church representatives. There, he expressed the view that although he personally opposed FGM, he regarded its legal abolition as counter-productive, and that the churches should focus on eradicating the practice through education of its harmful effects on women's health. The meeting ended without compromise, and John Arthur—the head of the Church of Scotland in Kenya—later complained about what he described as Kenyatta's dishonesty during the debate, expelling him from the church. In 1931, Kenyatta took his son out of the church school at Thogota and enrolled him in a KCA-approved, independent school.

In May 1931, Kenyatta and Parmenas Mockerie set sail for Europe, intent on representing the KCA as a joint select committee of parliament on the Future of East Africa. Kenyatta would not return to Kenya for fifteen years. In Britain, he spent the summer attending ILP summer schools and gatherings of the Fabian Society. In June, he visited Geneva, Switzerland to attend a conference on African children run by the Save the Children charity. In November, he met the Indian independence leader Mohandas Gandhi while in London. That month, he enrolled in the Woodbrooke Quaker College in Birmingham, where he remained until the spring of 1932, attaining a certificate in English writing.

In Britain, Kenyatta befriended an Afro-Caribbean Marxist, George Padmore, who was working for the Soviet-run Comintern. Over time, he became Padmore's protégé. In late 1932, he joined Padmore in Germany. Before the end of the year, the duo relocated to Moscow, where Kenyatta was instructed in becoming a professional revolutionary at the Communist University of the Toilers of the East. There, he was among those students who complained about the food, accommodation, and poor quality of English instruction. During his time in the Soviet Union, Kenyatta also visited Siberia, probably as part of an official guided tour. The emergence of the Nazi administration in Germany shifted political allegiances in Europe, as the Soviet Union sought to establish formal alliances with France and Czechoslovakia, thereby reducing its support for the movement against British and French colonial rule in Africa. As a result, Comintern disbanded the International Trade Union Committee of Negro Workers, to which both Padmore and Kenyatta were affiliated. Padmore resigned from the Communist Party of the Soviet Union in protest, and was subsequently vilified in the Soviet press. Both Padmore and Kenyatta left the Soviet Union, with the latter returning to London in August 1933.

Kenyatta had continued writing articles, in which he reflected Padmore's influence. He produced an article for a January 1933 issue of the Negro Worker, and then another for a November 1933 issue of Labour Monthly. He also wrote the entry on Kenya for Negro, an anthology edited by Nancy Cunard and published in 1934. In these, he took a more extreme position than he had in the past, calling for complete self-rule in Kenya. In doing so he was virtually alone among political Kenyans, with figures like Thuku and Jesse Kariuki being far less radical in their demands. The pro-independence sentiments that he was able to express in Britain would not have been permitted in Kenya itself.

Kenyatta was a Pan-Africanist. Assensoh suggested that Kenyatta initially had socialist inclinations but "became a victim of capitalist circumstances"; conversely, Savage stated that "Kenyatta's direction was hardly towards the creation of a radical new socialist society". When in power, he displayed a preoccupation with individual and mbari land rights that were at odds with any socialist-oriented collectivisation. He had been exposed to Marxist-Leninist ideas through his friendship with Padmore and the time spent in the Soviet Union, but had also been exposed to Western forms of liberal democratic government through his many years in Britain. He had been influenced by Marxist frameworks for analysing society, for instance in developing the belief that British colonialism had to be destroyed rather than simply reformed. However, he disagreed with the Marxist attitude that tribalism was backward and retrograde; his positive attitude toward tribal society frustrated some of Kenyatta's Marxist Pan-Africanist friends in Britain, among them Padmore, James, and Ras T. Makonnen, who regarded it as parochial and un-progressive. He appears to have had no further involvement with the communist movement after 1934.

In 1935, Italy invaded Ethiopia (Abyssinia), incensing Kenyatta and other Africans in London; he became the honorary secretary of the International African Friends of Abyssinia, a group established by Padmore and C. L. R. James. When Ethiopia's monarch Haile Selassie fled to London in exile, Kenyatta personally welcomed him. This group developed into a wider pan-Africanist organisation, the International African Service Bureau (IASB), which Kenyatta joined. Kenyatta began giving anti-colonial lectures across Britain for groups like the IASB and the Workers' Educational Association. In October 1938, he gave a talk to the Manchester Fabian Society in which he described British colonial policy as fascism and compared the treatment of indigenous people in East Africa to the treatment of Jews in Nazi Germany. In response to these activities, the British Colonial Office reopened their file on him, although could not find any evidence that he was engaged in anything sufficiently seditious to warrant prosecution.

Kenyatta assembled the seminar papers on Kikuyu society that he had written for Malinowski's class, publishing these as Facing Mount Kenya in 1938. Malinowski wrote an introduction for the book, while the jacket cover featured an image of Kenyatta in traditional dress, wearing a skin cloak over one shoulder and carrying a spear. The book was published under the name "Jomo Kenyatta", the first time that he had done so; the term Jomo was close to a Kikuyu word describing the removal of a sword from its scabbard. Facing Mount Kenya was a commercial failure, selling only 517 copies, but was generally well received; an exception was among white Kenyans, whose assumptions about the Kikuyu it challenged.

As a result of the war, communication between Kenya and Britain was greatly curtailed, and the Kenyan authorities banned the KCA in 1940. Towards the end of the conflict, Kenyatta was becoming restless and frustrated by the distance between him and Kenya. To Edna, he stated that he felt "like a general separated by 5000 miles from his troops". While in Sussex, he wrote an essay for the United Society for Christian Literature, My People of Kikuyu and the Life of Chief Wangombe, in which he called for his tribe's political independence. He also began—although never finished—a novel partly based on his life experiences. He continued to give lectures around the country, including to groups of East African Soldiers stationed in Britain.

After the United Kingdom entered World War II in September 1939, Kenyatta and Stock left London for the village of Storrington in Sussex. There, Kenyatta remained for the duration of the war, renting a flat and a small plot of land to grow vegetables and raise chickens. He settled into rural Sussex life, and became a regular at the village pub, where he gained the nickname "Jumbo". In August 1940, he took a job at a local farm as an agricultural worker; this allowed him to evade military conscription. He later worked at the tomato houses at Lindfield. He also attempted to join the local Home Guard, but was turned down. He began a relationship with an English woman, Edna Grace Clarke, and they married at Chanctonbury Registry Office on 11 May 1942. On 11 August 1943, their son, Peter Magana, was born.

In August 1944, the Kenya African Union (KAU) had been founded as the only political outlet for indigenous Africans in the colony. At its June 1947 annual general meeting, KAU's President James Gichuru stepped down and Kenyatta was elected as his replacement. Kenyatta began to draw large crowds wherever he travelled in Kikuyuland, and Kikuyu press began describing him as the "Saviour", "Great Elder", and "Hero of Our Race". He was nevertheless aware that for independence to be achieved, KAU would need the support of other indigenous tribes and ethnic groups. This was made difficult by the fact that many Masai and Luo—tribes traditionally hostile to the Kikuyu—regarded him as an advocate of Kikuyu dominance. He insisted on intertribal representation on the KAU executive and ensured that party Business was conducted in Swahili, a language spoken by many groups.

Kenyatta and other senior IASB members began planning the fifth Pan-African Congress, held in Manchester in October 1945. They were assisted by Kwame Nkrumah, a West African who arrived in Britain earlier that year. Kenyatta spoke at the conference, although made no particular impact on the proceedings. Much of the debate that took place centred on whether indigenous Africans should continue pursuing a gradual campaign for independence or whether they should seek the military overthrow of the European imperialists. The conference ended with a statement declaring that while delegates desired a peaceful transition to African self-rule, Africans "as a last resort, may have to appeal to force in the effort to achieve Freedom". Kenyatta supported this resolution, although was more cautious than other delegates and made no open commitment to violence. He subsequently authored an IASB pamphlet, Kenya: The Land of Conflict, in which he again blended political calls for independence with romanticised descriptions of an idealised pre-colonial African past.

After British victory in World War II, Kenyatta received a call to return to Kenya in September 1946, sailing back that month. Edna was pregnant with a second child, although she expected to never see her husband again; Kenyatta was aware that if they joined him in Kenya their lives would be made very difficult by the colony's racial laws. On his arrival in Mombasa, Kenyatta was greeted by his first wife and their children. He built a bungalow at Gatundu, near to where he was born, and began farming his 32-acre estate. Kenyata met with the new Governor of Kenya, Philip Euen Mitchell, and in March 1947 accepted a post on an African Land Settlement Board, holding the post for two years. He also met with Mbiyu Koinange to discuss the Future of the Koinange Independent Teachers' College in Githungui, with Koinange appointing Kenyatta as its Vice-Principal. In May 1947, Koinange moved to England, leaving Kenyatta to take full control of the college. Under Kenyatta's leadership, additional funds were raised for the construction of school buildings and the number of boys in attendance rose from 250 to 900. It was also beset with problems, including a decline in standards and teachers' strikes over non-payment of wages. Gradually, the number of enrolled pupils fell. Kenyatta built a friendship with Koinange's father, a Senior Chief, who gave Kenyatta one of his daughters to take as his third wife. She bore him another child, but later died in childbirth. In 1951, he married his fourth wife, Ngina, who was one of the few female students at his college. She gave birth to a daughter.

During much of his life, Kenya's white settlers had regarded Kenyatta as a malcontent and an agitator. As noted by Arnold, "no figure in the whole of British Africa, with the possible exception of [Nkrumah], excited among the settlers and the colonial authorities alike so many expressions of anger, denigration and fury as did Kenyatta." As the Historian Keith Kyle put it, for many whites Kenyatta was "Satan Incarnate". This white animosity reached its apogee between 1950 and 1952. By 1964, this image had largely shifted, with many white settlers referring to him as "Good Old Mzee". Murray-Brown expressed the view that for many, Kenyatta's "message of reconciliation, 'to forgive and forget', was perhaps his greatest contribution to his country and to history."

In October 1952, Kenyatta was arrested at his Githunguri home and driven to Nairobi, where he was taken aboard a plane and flown to Lokitaung, one of the most remote locations in the country. From there he was allowed to write to his family to let them know of his situation. The Kenyan authorities believed that detaining Kenyatta would help to quell the civil unrest. Many white settlers wanted him exiled, a course of action that the government feared would turn him into a martyr for the anti-colonialist cause. They thought it better that he be convicted and imprisoned, although at the time of his detainment had nothing to charge Kenyatta with, and so began looking through his personal files for evidence of any involvement in Criminal activity. Eventually, they charged both him and five senior KAU members with masterminding the Mau Mau guerrillas, which were a proscribed group. The Historian A. B. Assensoh later suggested that the authorities "knew very well" that Kenyatta was not involved in the Mau Mau, but that they were nevertheless committed to silencing his calls for independence. While contemporary opinion linked Kenyatta with the Mau Mau, historians have questioned his alleged leadership of the radical movement.

In remand status, Kenyatta and the others were returned to Lokitaung, where they resided in huts while awaiting the results of the appeal process. Pritt pointed out that Thacker had been appointed magistrate for the wrong district, a technicality that meant the whole trial was void; the Supreme Court of Kenya concurred and Kenyatta and the others were freed in July 1953, although immediately re-arrested. The government then took the case the East African Court of Appeal, which reversed the Supreme Court's decision in August. The appeals process resumed in October 1953, and in January 1954 the Supreme Court upheld the convictions against all but Oneko. Pritt finally took the case to the Privy Council in London, but they refused his petition without providing an explanation. He later noted that this was despite the fact his case was one of the strongest he had ever presented during his career. It is likely that political, rather than legal considerations, informed their decision to reject the case.

Kenyatta's imprisonment transformed him into a political martyr for many Kenyans, further enhancing his status. A Luo anti-colonial Activist, Jaramogi Oginga Odinga, was the first to publicly call for Kenyatta's release, an issue that gained growing support among Kenya's anti-colonialists. In 1955, the British Writer Montagu Slater—a socialist sympathetic to Kenyatta's plight—released The Trial of Jomo Kenyatta, a book which raised the profile of the case. By the late 1950s, the imprisoned Kenyatta had become a symbol of African nationalism across the continent. Calls for his release were being made outside Kenya: resolutions to that effect were produced at the All-African Peoples' Conferences held in Tunis in 1960 and Cairo in 1961. Tanganyikan President Julius Nyerere also did so. Activists in the Kenyan Asian community also backed him, with the Kenya Indian Congress calling for his release. In April 1959, Kenyatta was released from Lokitaung. The administration then placed a restricting order on Kenyatta, forcing him to reside in the remote area of Lodwar, where he had to report to the district commissioner twice a day. There, he was joined by his wife Ngina. In October 1961 she bore him another son, Uhuru, and later on another daughter, Nyokabi, and a further son, Muhoho. Kenyatta spent two years in Lodwar.

After the Lancaster House negotiations, the anti-colonial movement had split into two parties, the Kenya African National Union (KANU), which was dominated by Kikuyu and Luo, and the Kenya African Democratic Union (KADU), which was led largely by members of smaller tribal groups. In May 1960, KANU nominated Kenyatta as its President, although the government vetoed it, insisting that he had been an instigator of the Mau Mau. KANU then declared that it would refuse to take part in any government unless Kenyatta was freed. KANU campaigned on the issue of Kenyatta's detainment in the February 1961 election, where it gained a majority of votes. KANU nevertheless refused to form a government, which was instead created through a KADU-led coalition of smaller parties. Kenyatta had kept abreast of these developments, although refused to back either KANU or KADU, instead insisting on unity between the two parties.

After his release, Kenyatta set about trying to ensure that he was the only realistic option as Kenya's Future leader. In August he met with the Governor of Kenya, Patrick Muir Renison, at Kiambu, and he was interviewed by the BBC's Face to Face program. In August he also attended a KANU-KADU meeting, where the two parties disagreed on the question of federalism: KANU wanted a centralised state while KADU feared that this would result in Kikuyu dominance of an independent Kenya. In October 1961, Kenyatta accepted the KANU Presidency, and in January 1962 was elected unopposed as the KANU representative for the Fort Hall constituency in the legislative council after its sitting member, Kariuki Njiiri, resigned.

Kenyatta sought to gain the confidence of the white settler community. In 1962, the white minority had produced 80% of the country's exports and were a vital part of its economy, yet between 1962 and 1963 they were leaving Kenya at a rate of 700 a month; Kenyatta feared that this white exodus would cause a brain drain and skills shortage that would be detrimental to the economy. He was also aware that the confidence of the white minority would be crucial to securing Western investment in Kenya's economy. Kenyatta made it clear that when in power, he would not sack any white civil servants unless there were competent black individuals capable of replacing them. He was sufficiently successful that a number of prominent white Kenyans backed KANU in the subsequent election. A key issue facing Kenya was a border dispute in North East Province, alongside Somalia. Ethnic Somalis inhabited this region and claimed that it should be part of Somalia, not Kenya. Kenyatta refused to accede to their demands, insisting that the land remain Kenyan. In June 1962 Kenyatta travelled to Mogadishu to discuss the issue with the Somalian authorities, but the two sides could not reach an agreement.

A celebration to mark independence was held in a specially constructed stadium on 12 December 1963. During the ceremony, Prince Philip, Duke of Edinburgh—representing the British monarchy—formally handed over control of the country to Kenyatta. Also in attendance were leading figures from the Mau Mau. In a speech, Kenyatta described it as "the greatest day in Kenya's history and the happiest day in my life." He had flown Edna and Peter over for the ceremony, and in Kenya they were welcomed into Kenyatta's family by his other wives. Kenyatta nevertheless faced domestic opposition and in January 1964, sections of the army launched a mutiny in Nairobi, with Kenyatta calling on the British Army to put down the rebellion. Similar armed uprisings had taken place in neighbouring Uganda and Tanganyika. Kenyatta publicly rebuked the mutineers, emphasising the need for law and order in Kenya. At Kenyatta's prompting, in November 1964, KADU officially dissolved and its representatives joined KANU. Two of the senior members of KADU, Ronald Ngala and Daniel arap Moi, subsequently became some of Kenyatta's most loyal supporters in KANU. Kenya therefore became a de facto one-party state.

Facing the pressures of the Cold War, Kenyatta officially pursued a policy of "positive non-alignment". In reality, his foreign policy was pro-Western and in particular pro-British. Kenya became a member of the British Commonwealth, using this as a vehicle to put pressure on the white-minority apartheid regimes in South Africa and Rhodesia. Britain remained one of Kenya's foremost sources of foreign trade; British aid to Kenya was among the highest in Africa. In 1964, Kenya and the UK signed a Memorandum of Understanding, one of only two military alliances that Kenyatta's government made. Various commentators argued that Britain's relationship with Kenyatta's Kenya was a neo-colonial one, with the British having exchanged their position of political power for one of influence. The Historian Poppy Cullen nevertheless noted that there was no "dictatorial neo-colonial control" in Kenyatta's Kenya. Although many white Kenyans had come to accept his rule, he remained opposed by far right activists; while in London at the July 1964 Commonwealth Conference, Kenyatta was assaulted by Martin Webster, a British Neo-Nazi. Kenyatta also maintained a warm relationship with Israel, including when other East African nations had endorsed Arab hostility to the state; he for instance permitted Israeli jets to refuel in Kenya on their way back from the Entebbe raid.

A major focus for Kenyatta during the first three and a half years of Kenya's independence were the divisions within KANU itself. Opposition to Kenyatta's government grew, particularly following the assassination of Pio Pinto in February 1965. Relations between Kenyatta and Odinga were strained, and at the March 1966 party conference, Odinga's post—that of party Vice President, was divided among eight different politicians. In 1966, Odinga stepped down as state Vice President, claiming that Kenya had failed to achieve economic independence and needed to adopt truly socialist policies. Backed by several other senior KANU figures and trade unionists, he formed the Kenya Peoples Union (KPU). The KPU were legally recognised as the official opposition, thus restoring the country's two party system.

Kenyatta's government resorted to un-democratic measures to restrict the opposition. It used laws on detention and deportation to perpetuate its own political hold in the country. In 1966, it passed the Public Security (Detained and Restricted Persons) Regulations, allowing the authorities to arrest and detain anyone "for the preservation of public security" without putting them on trial. The government banned the KPU, and arrested Odinga before putting him under indefinite detainment. Many other figures were also indefinitely detained, including the prominent author Ngũgĩ wa Thiong'o. Other political figures who were critical of Kenyatta's administration, including Ronald Ngala and Josiah Mwangi Kariuki, were killed in incidents that many speculated were government assassinations. With the organised opposition eliminated, from 1969, Kenya was once again a de facto one-party state.

In part due to his advanced years, Kenyatta rarely travelled outside of Eastern Africa. Under Kenyatta, Kenya was largely uninvolved in the affairs of other states, including those in the East African Community. Despite his reservations about any immediate East African Federation, in June 1967 Kenyatta signed the Treaty for East African Co-operation. In December he attended a meeting with Tanzanian and Ugandan representatives to form the East African Economic Community, reflecting Kenyatta's cautious approach toward regional integration. He also took on a mediating role during the Congo Crisis, heading the Organisation of African Unity's Conciliation Commission on the Congo.

The Kenyan government had been preparing for Kenyatta's death since at least his 1968 stroke; it had requested British assistance in organising his state funeral as a result of the UK's longstanding experience in this area. McKenzie had been employed as a go-between, and the structure of the funeral was orchestrated to deliberately imitate that of deceased British Prime Minister Winston Churchill. In doing so, senior Kenyans sought to project an image of their country as a modern nation-state rather than one incumbent on tradition. The funeral took place at St. Andrew's Presbyterian Church, six days after Kenyatta's death. Britain's heir to the throne, Charles, Prince of Wales, attended the event, a symbol of the value that the British government perceived in its relationship with Kenya.

In July 1969, the prominent Luo Politician Mboya was assassinated by a Kikuyu, with suspicions being voiced that Kenyatta's government had been responsible. The killing sparked riots in Nairobi, and ethnic tensions were stoked across Kenya. In October 1969, Kenyatta visited Kisumu, located in Luo territory, in order to open a hospital financed with Soviet aid. He was greeted by a crowd shouting KPU slogans and he lost his temper. When members of the crowd started throwing stones, Kenyatta's Bodyguards opened fire on them, killing and wounding several. In response to the rise of KPU, Kenyatta had introduced oathing, a system in which individuals came to Gatundu to swear their loyalty to him. Journalists were discouraged from reporting on the oathing system, and several were deported when they tried to do so. Many were pressured or forced to conduct the oaths, generating a condemnation from the country's Christian establishment. In response to the growing condemnation, the oathing was terminated in September 1969, and Kenyatta invited Leaders from other ethnic groups to a meeting in Gatundi.

Within Kenya, Kenyatta came to be regarded as the "Father of the Nation", viewed as a father figure by Kikuyu, Kenyans, and Africans more widely. In Kenya, he became a popular symbol of the nation itself, something furthered by the similarities between their names, while he was also given the unofficial title of Mzee, a Swahili term meaning "grand old man". In 1974, Guy Arnold referred to Kenyatta as "one of the outstanding African Leaders now living", someone who had become "synonymous with Kenya". He added that Kenyatta had been "one of the shrewdest politicians" on the continent, regarded as "one of the great Architects of African nationalist achievement since 1945". Kenneth O. Nyangena described him as "one of the greatest men of the twentieth century", having been "a beacon, a rallying point for suffering Kenyans to fight for their rights, justice and freedom" whose "brilliance gave strength and aspiration to people beyond the boundaries of Kenya". In their examination of his writings, Bruce J. Berman and John M. Lonsdale described him as a "pioneer" for being one of the very first Kikuyu to write and publish; "his representational achievement was unique".

Kenyatta had a mild stroke in 1966, and then a second stroke in May 1968. On 22 August 1978, Kenyatta died in the State House, Mombasa.

Assensoh argued that in his life story, Kenyatta had a great deal in Common with the Ghanaian leader, Nkrumah. Simon Gikandi noted that Kenyatta, like Nkrumah, was remembered for "initiating the discourse and process that plotted the narrative of African freedom", but at the same time both were "often remembered for their careless institution of presidential rule, one party dictatorship, ethnicity and cronyism. They are remembered both for making the dream of African independence a reality and for their invention of postcolonial authoritarianism." In 1991, the Kenyan Lawyer and human rights Activist Gibson Kamau Kuria noted that in abolishing the federal system, banning independent candidates from standing in elections, setting up a unicameral legislature, and relaxing restrictions on the use of emergency powers, Kenyatta had laid "the groundwork" for Moi to further advance dictatorial power in Kenya during the late 1970s and 1980s.

Kenyatta was accused by Kenya's Truth, Justice and Reconciliation Commission in its report released in May 2013 of using his authority as President to allocate large tracts of land to himself and his family across Kenya. The Kenyatta family is among Kenya's biggest landowners. During the 1990s, there was still much frustration among various tribal groups, namely in the Nandi, Nakuru, Uasin-Gishu, and Trans-Nzoia Districts, that under Kenyatta's government they had not regained the lands taken by European settlers and that more of their land had been sold to those regarded as "foreigners"—Kenyans from other tribes. Among these groups there were widespread calls for restitution and in 1991 and 1992 there were violent attacks against many of those who obtained land through Kenyatta's patronage in these areas. The violence continued sporadically until 1996, with an estimated 1500 killed and 300,000 displaced in the Rift Valley. Kenyatta's government also made little progress in advancing women's rights in Kenya, where women remained second-class citizens.

Towards the end of his Presidency, many younger Kenyans—while respecting Kenyatta's role in attaining independence—were regarding him as a reactionary. Those desiring radical transformation of Kenyan society often compared Kenyatta's Kenya unfavourably with its southern neighbour, Nyerere's Tanzania. The criticisms that leftists like Odinga made of Kenyatta's leadership were similar to those that the intellectual Frantz Fanon had made of post-colonial Leaders throughout Africa. Drawing upon Marxist theory, Jay O'Brien for instance argued that Kenyatta had come to power "as a representative of a would-be bourgeoisie", a coalition of "relatively privileged petty bourgeois African elements" who desired to replace the British colonialists and "Asian commercial bourgeoisie". He suggested that the British supported Kenyatta in this, seeing him as a bulwark against growing worker and peasant militancy who would ensure continued neo-colonial dominance.