With first settlements occurring in 1635, the first towns were Maspeth (est. 1642), Vlissingen (now Flushing, est. 1643) as well as Newtown (now Elmhurst) and Rustdorp (now Jamaica). While these towns were all in New Netherlands and under the auspices of Dutch law, the settlers tended to be English.

Many of these settlers were seeking religious freedom in the New World, Holland, in particular, was known for its religious tolerance and these settlers expected their colonies would be to. However, Peter Stuyvesant had a different idea and banned the practice of all but the Dutch Reformed Church. This spurred ample conflict between the Dutch authorities and the foreign settlers.

This famously came to a head in the 1657 Flushing Remonstrance, widely thought to be a precursor to the bill of rights provision on freedom of religion. The thirty residents of Vlissingen appealed to Stuyvesant for an exemption on the ban of the Quaker faith. While Stuyvesant's response was harsh, replacing the town's government and imprisoning some of the signers, his eventual banishment of John Bowne (for continuing to hold Quaker meetings) resulted in the Dutch East India company ordering Stuyvesant to end religious intolerance in 1663.

However, Peter Stuyvesant's days of importance were at an end. By October of 1664, the English had seized the New Netherland territory (an action that helped start the Second Anglo-Dutch War.) While New Netherland would be retaken briefly in 1673, it remained in defacto British control from 1664 and in 1674 was ceded to England.

When the state of New York was created on November 1st, 1683, Queens was one of the original twelve counties. It is thought that the name Queens stemmed from the Queen of England at the time: Catherine of Braganza.

During the Revolutionary War, Queens was largely quiet. With most of the fighting during the war occurring in Brookly and Manhattan, British forces quietly occupied Queens (which was largely loyalist.) The famous spy Nathan Hale was apprehended in Queens on Flushing Bay, though he was hung in Manhattan.

Queens County, following the war, remained largely agricultural and rural. However, the seeds of change were coming and by the 1850 census the western towns' population (in present-day Queens) began to outnumber that of the eastern town (in present-day Nassau County.) Furthermore, the west began to build factories and industrialize, while the east remained fairly rural.

With the west of Nassau County burgeoning in importance, the county seat was moved from Mineola to Long Island City and the courthouse with it. This was indicative of the area's growth, sporting its own school system, water supply, and police force. However, the eastern towns resented this change as they felt further from the center of power in the county.

Consolidation was the final straw. With the western towns of Queens joining New York City in 1898, the rest of Queens was left in limbo: part of the county of Queens, but not part of the Borough. Moreover, the consolidation plan called for the dissolving of all local and county governments. In 1899, the New York State legislature agreed to let the eastern part of Queens form their own county and Nassau County was born.