In 1813, Cooper married Sarah Bedell (1793–1869). Of their six children, only two survived past the age of four years: a son, Edward and a daughter, Sarah Amelia. Edward served as Mayor of New York City, as would the husband of Sarah Amelia, Abram S. Hewitt, a man also heavily involved in inventions and industrialization.

In 1821 Cooper purchased a glue factory on Sunfish Pond for $2,000 in Kips Bay, where he had access to raw materials from the nearby slaughterhouses, and ran it as a successful Business for many years, producing a profit of $10,000 (equivalent to roughly $200,000 today) within 2 years, developing new ways to produce glues and cements, gelatin, isinglass and other products, and becoming the city's premier provider to tanners, manufacturers of paints, and dry-goods merchants. The effluent from his successful factory eventually polluted the pond to the extent that in 1839 it had to be drained and refilled.

Having been convinced that the proposed Baltimore and Ohio Railroad would drive up prices for land in Maryland, Cooper used his profits to buy 3,000 acres (12 km) of land there in 1828 and began to develop them, draining swampland and flattening hills, during which he discovered iron ore on his property. Seeing the B&O as a natural market for iron rails to be made from his ore, he founded the Canton Iron Works in Baltimore, and when the railroad developed technical problems, he put together the Tom Thumb steam locomotive for them in 1830 from various old parts, including musket barrels, and some small-scale steam engines he had fiddled with back in New York. The engine was a rousing success, prompting Investors to buy stock in B&O, which enabled the company to buy Cooper's iron rails, making him what would be his first fortune.

Cooper began operating an iron rolling mill in New York beginning in 1836, where he was the first to successfully use anthracite coal to puddle iron. Cooper later moved the mill to Trenton, New Jersey on the Delaware River to be closer to the sources of the raw materials the works needed. His son and son-in-law, Edward Cooper and Abram S. Hewitt, later expanded the Trenton facility into a giant complex employing 2,000 people, in which iron was taken from raw material to finished product.

In 1840, Cooper became an alderman of New York City.

Cooper had for many years held an interest in adult education: he had served as head of the Public School Society, a private organization which ran New York City's free schools using city money, when it began evening classes in 1848. Cooper conceived of the idea of having a free institute in New York, similar to the École Polytechnique (Polytechnical School) in Paris, which would offer free practical education to adults in the mechanical arts and science, to help prepare young men and women of the working classes for success in Business.

Cooper later invested in real estate and insurance, and became one of the richest men in New York City. Despite this, he lived relatively simply in an age when the rich were indulging in more and more luxury. He dressed in simple, plain clothes, and limited his household to only two servants; when his wife bought an expensive and elaborate carriage, he returned it for a more sedate and cheaper one. Cooper remained in his home at Fourth Avenue and 28th Street even after the New York and Harlem Railroad established freight yards where cattle cars were parked practically outside his front door, although he did move to the more genteel Gramercy Park development in 1850.

In 1851, Cooper was one of the founders of Children's Village, originally an orphanage called "New York Juvenile Asylum", one of the oldest non-profit organizations in the United States.

In 1853, he broke ground for the Cooper Union for the Advancement of Science and Art, a private college in New York, completing the building in 1859 at the cost of $600,000. Cooper Union offered open-admission night classes available to men and women alike, and attracted 2,000 responses to its initial offering, although 600 later dropped out. The classes were non-sectarian, and women were treated equally with men, although 95% of the students were male. Cooper started a Women's School of Design, which offered daytime courses in engraving, lithography, painting on china and drawing.

In 1854, Cooper was one of five men who met at the house of Cyrus West Field in Gramercy Park to form the New York, Newfoundland and London Telegraph Company, and, in 1855, the American Telegraph Company, which bought up competitors and established extensive control over the expanding American network on the Atlantic Coast and in some Gulf coast states. He was among those supervising the laying of the first Transatlantic telegraph cable in 1858.

Cooper's efforts led to the formation of the Board of Indian Commissioners, which oversaw Ulysses S. Grant's Peace Policy. Between 1870 and 1875, Cooper sponsored Indian delegations to Washington, D.C., New York City, and other Eastern cities. These delegations met with Indian rights advocates and addressed the public on United States Indian policy. Speakers included: Red Cloud, Little Raven, and Alfred B. Meacham and a delegation of Modoc and Klamath Indians.

Cooper was a Unitarian who regularly attended the services of Henry Whitney Bellows, and his views were Universalistic and non-sectarian. In 1873 he wrote:

Cooper was encouraged to run in the 1876 presidential election for the Greenback Party without any hope of being elected. His running mate was Samuel Fenton Cary. The campaign cost more than $25,000. At the age of 85 years, Cooper is the oldest person ever nominated by any political party for President of the United States. The election was won by Rutherford Birchard Hayes of the Republican Party. Cooper was surpassed by another unsuccessful candidate: Samuel Jones Tilden of the Democratic Party.

Cooper died on April 4, 1883 at the age of 92 and is buried in Green-Wood Cemetery in Brooklyn, New York.

Peter Cooper's granddaughters, Sarah Cooper Hewitt, Eleanor Garnier Hewitt and Amy Hewitt Green founded the Cooper-Hewitt National Design Museum, then named the Cooper-Hewitt Museum, in 1895. It was originally part of Cooper Union, but since 1967 has been a unit of the Smithsonian Institution.

Cooper also operated a successful glue factory in Gowanda, New York that produced glue for decades. A glue factory was originally started in association with the Gaensslen Tannery, there, in 1874, though the first construction of the glue factory's plant, originally owned by Richard Wilhelm and known as the Eastern Tanners Glue Company, began on May 5, 1904. Gowanda, therefore, was known as America's glue capital.

Today Cooper Union is recognized as one of the leading American colleges in the fields of architecture, engineering, and art. Carrying on Peter Cooper's belief that college education should be free, the Cooper Union awarded all its students with a full scholarship until fall 2014.