In 1898, Yonkers (along with Brooklyn, Queens, and Staten Island) voted on a referendum to determine if they wanted to become part of New York City.While the results were positive elsewhere, the returns were so negative in Yonkers and neighboring Mount Vernon that those two areas were not included in the consolidated city, and remained independent.

All the lands that belonged to the Philipse family were confiscated and sold.

For its first two hundred years, Yonkers was a small farming town with an active industrial waterfront.

Frederick was a wealthy Dutchman who by the time of his death had amassed an enormous estate, which encompassed the entire modern City of Yonkers, as well as several other Hudson River towns.

Philipse's great-grandson, Frederick Philipse III, was a prominent Loyalist during the American Revolution, who, because of his political leanings, was forced to flee to England.

The land on which the city is built was once part of a 24,000-acre (97-square-kilometer) land grant called Colen Donck that ran from the current Manhattan-Bronx border at Marble Hill northwards for 12 miles (19 km), and from the Hudson River eastwards to the Bronx River.

This grant was purchased in July 1645 by Adriaen van der Donck, the first lawyer in North America.

The Alexander Smith Carpet Company, one of the city's largest employers, ceased operation during a labor dispute in June 1954.

In 1983, the Otis Elevator Factory finally closed its doors.

Van der Donck was known locally as the Jonkheer or Jonker (etymologically, "young gentleman," derivation of old Dutch jong (young) and heer ("lord"); in effect, "Esquire"), a word from which the name "Yonkers" is directly derived.

Van der Donck built a saw mill near where the Nepperhan Creek met the Hudson; the Nepperhan is now also known as the Saw Mill River. His wife, Mary Doughty, was taken captive and ransomed later.

In 1888, Scottish-born John Reid founded the first golf course in the United States, St. Bakelite, the first completely synthetic plastic, was invented in Yonkers circa 1906 by Leo Baekeland, and manufactured there until the late 1920s.