The story begins with a man named John Bowne. Bowne was an English immigrant to the Dutch colony of New Amsterdam, who settled in Flushing (originally called Vlissingen) in the early 1660s. He and his first wife converted to Quakerism after marriage, and their move to Flushing was motivated by a desire to join the English-speaking Society of Friends there.

In 1662, Bowne was arrested on the orders of Dutch Governor Peter Stuyvesant for having a Quaker meeting in his home. Stuyvesant had long persecuted the Quaker communities of New York. Bowne was sent to the Netherlands, and despite not speaking any Dutch, appealed to the Dutch West India Company for freedom.

His arrest had followed the Flushing Remonstrance, in which the thirty residents of Flushing (then called Vlissingen), had demanded the freedom to practice any religion. After some deliberation, the Dutch East India Company decided to side with Bowne and ordered Stuyvesant to stop religious persecution. With his release, a new precedent was set for religious tolerance and freedom in the colony.

Emboldened by this new religious freedom, the community built a formal spaceto worship. The Old Quaker Meeting House is one of the oldest houses of worship in New York State. At least one-third of the current building (the section closest to Union Street) dated to 1694 when the wood-frame structure was constructed on land purchased by John Bowne and John Rodman. The building was expanded in 1716 and 1719. The particularly steep roof is evocative of medieval Dutch architecture, and the interiors remain in the simple style of the Society of Friends: dark floorboards and plain benches.

Bowne also donated land for a Quaker Cemetary next to the meeting house. This 1925 photograph captures a view of the cemetery and the meeting house. During the early years after the founding of the Meeting House, an unknown number of Quakers were buried here without headstones, as was the custom of the time. During the 18th century, burials began to be accompanied by simple stones that usually only noted a name or initials.

The Meeting House continues to be the place of worship for the Flushing Meeting of the Religious Society of Friends. It has served this purpose for more than 300 years

The home where Bowne was arrested still stands. Likely built-in 1661 (a year before his arrest), it is a wood-frame home of Dutch design but constructed with English building techniques. The home was altered, unsurprisingly, a number of times in the centuries since it was built. Members of the Bowne family continued to live in the home until 1945 when they sold it to the newly-created Bowne House Historical Society, which opened it as a museum in 1947 and continues to operate it today.