Cleaver was a presidential candidate in 1968 on the ticket of the Peace and Freedom Party. Having been born on August 31, 1935, Cleaver would not have been the requisite 35 years of age until more than a year after Inauguration Day 1969. (Although the Constitution requires that the President be 35 years of age, it does not specify if he need have reached that age at the time of nomination, or election, or inauguration.) Courts in both Hawaii and New York held that he could be excluded from the ballot because he could not possibly meet the Constitutional criteria. Cleaver and his running mate Judith Mage received 36,571 votes (0.05%).

Cleaver was released from prison on December 12, 1966. He was writing for Ramparts magazine and organizing efforts to revitalize the Organization of Afro-American Unity. At this time, President John F. Kennedy and Malcolm X were dead. The Black Panther Party was only two months old. He then joined the Oakland-based Black Panther Party (BPP), serving as Minister of Information, or spokesperson. What initially attracted Cleaver to the Panthers, as opposed to other prominent groups, was their commitment to armed struggle.

Charged with attempted murder, he jumped bail to flee to Cuba in late 1968. There, he received red-carpet treatment. Cleaver was set up in a Havana penthouse with his own personal maid and cook. The penthouse was stocked with all the food, rum, and cigars he would need. The hospitality soon ended. Having received information that the CIA had infiltrated the Black Panther Party, Castro could no longer trust them. Cleaver then decided to head to Algeria, sending word to his wife to meet him there. Cleaver had set up an international office for the Black Panthers in Algeria. Following Timothy Leary's Weather Underground-assisted prison escape, Leary stayed with Cleaver in Algeria; however, Cleaver placed Leary under "revolutionary arrest" as a counter-revolutionary for promoting drug use.

Cleaver also cultivated an alliance with North Korea in 1969, and BPP publications began reprinting excerpts from Kim Il Sung's writings. Although leftists of the time often looked to Cuba, China, and North Vietnam for inspiration, few had paid any attention to the secretive Pyongyang regime. Bypassing US travel restrictions on North Korea, Cleaver and other BPP members made two visits to the country in 1969-70 with the idea that the juche model could be adapted to the revolutionary liberation of African-Americans. Taken on an official tour of North Korea, Cleaver expressed admiration at "the DPRK's stable, crime-free society which provided guaranteed food, employment, and housing for all, and which had no economic or social inequalities".

In 1967, Cleaver, along with Marvin X, Ed Bullins, and Ethna Wyatt, formed the Black House political/cultural center in San Francisco. Amiri Baraka, Sonia Sanchez, Askia Toure, Sarah Webster Fabio, Art Ensemble of Chicago, Avotcja, Reginald Lockett, Emory Douglas, Samuel Napier, Bobby Hutton, Huey Newton, and Bobby Seale were Black House regulars. The same year, he married Kathleen Neal Cleaver (divorced 1987) with whom he would have son Ahmad Maceo Eldridge (b. 1969, Algeria) and daughter Joju Younghi (b. July 31, 1970, North Korea).

Eldridge Cleaver and Huey Newton eventually fell out with each other over the necessity of armed struggle as a response to COINTELPRO and other actions by the government against the Black Panthers and other radical groups. Also Cleaver's interest in North Korea and global anti-imperialist struggle drew ire from other BPP members who felt that he was neglecting the needs of African-Americans at home in the US. Following his expulsion from the Black Panthers in 1971, the group's ties with North Korea were quickly forgotten. Cleaver advocated the escalation of armed resistance into urban guerilla warfare, while Newton suggested the best way to respond was to put down the gun, which he felt alienated the Panthers from the rest of the black community, and focus on more pragmatic reformist activity by lobbying for increased social programs to aid African-American communities and anti-discrimination laws. Cleaver accused Newton of being an Uncle Tom for choosing to cooperate with white interests rather than overthrow them.

Cleaver left Algeria in 1972, moving to Paris, France, becoming a born again Christian during time in isolation living underground. He turned his hand to fashion design; three years later, he released codpiece-revival "virility pants" he called "the Cleavers", enthusing that they would give men "a chance to assert their masculinity".

After spending seven years in exile in Cuba, Algeria, and France, Cleaver returned to the US in 1975, where he became involved in various religious groups (Unification Church and CARP) before finally joining the Church of Jesus Christ of Latter-day Saints, as well as becoming a conservative Republican, appearing at Republican events.

Cleaver returned to the United States in 1977 to face the unresolved attempted murder charge. By September 1978, on bail as those proceedings dragged on, he had incorporated Eldridge Cleaver Ltd, running a factory and West Hollywood shop exploiting his "Cleavers", which he claimed liberated men from "penis binding". He saw no conflict with his newfound Christianity, drawing support for his overtly sexual design from 22 Deuteronomy. The long-outstanding charge was subsequently resolved on a plea bargain reducing it to assault. A sentence of 1,200 hours' community Service was imposed.

In his 1978 book Soul on Fire, Cleaver made several claims regarding his exile in Algeria, including that he was supported by regular stipends from the government of North Vietnam, which the United States was then bombing. Cleaver stated that he was followed by other former Criminals turned Revolutionaries, many of whom (including Booth and Smith) hijacked planes to get to Algeria.

By the 1980s, Cleaver had become a conservative Republican. He appeared at various Republican events and spoke at a California Republican State Central Committee meeting regarding his political transformation. In 1984, he ran for election to the Berkeley City Council but lost. Undaunted, he promoted his candidacy in the Republican Party primary for the 1986 Senate race but was again defeated. The next year, his 20-year marriage to Kathleen Neal Cleaver came to an end.

Cleaver was then later baptized into The Church of Jesus Christ of Latter-day Saints (LDS Church) on December 11, 1983, periodically attended regular services, lectured by invitation at LDS gatherings, and was a member of the Church in good standing at the time of his death in 1998.

In 1988, Cleaver was placed on probation for burglary and was briefly jailed later in the year after testing positive for cocaine. He entered drug rehabilitation for a stated crack cocaine addiction two years later, but was arrested for possession by Oakland and Berkeley Police in 1992 and 1994. Shortly after his final arrest, he moved to Southern California, falling into poor health.

On May 1, 1998, at 6:20 A.M., Cleaver, aged 62, died at Pomona Valley Hospital Medical Center in Pomona, California. CNN Obituary He is buried at Mountain View Cemetery in Altadena, California.

The essays in Soul on Ice are divided into four thematic sections: "Letters from Prison", describing Cleaver's experiences with and thoughts on crime and prisons; "Blood of the Beast", discussing race relations and promoting black liberation ideology; "Prelude to Love – Three Letters", love letters written to Cleaver's attorney, Beverly Axelrod; and "White Woman, Black Man", on gender relations, black masculinity, and sexuality.