In 1676, before the Meeting House was built, John Bowne donated land and arranged for a burial ground on Northern Boulevard. The Meeting House was built on land purchased adjacent to the graveyard in 1694. Today, after a great deal of expense and volunteer effort, the graveyard is cleared and blooms with indigenous flowers and bushes. Old elm trees and oaks shade the perimeter and help set the quiet garden apart from its bustling neighbors. It is a startlingly beautiful, peaceful place in the midst of downtown Flushing, and it is a perfect place to remember the Quakers who lived here before us, and who lived such extraordinary lives.

The early Quakers did not use headstones and so it is difficult to say who was buried in the Meeting House graveyard before 1820. It is believed that John Bowne is buried here, as the Bowne family plot is in the graveyard, but there is no existent headstone marking his grave. When Quakers did begin using headstones, they were often small and plain with no more than a name or initials on it. Many of these small stones have sunk into the earth or shifted out of position over the years. At least one stone was stolen.

A number of prominent early Quakers are buried here. Noted abolitionists William Burling and Matthew Franklin are here, as is Samuel Leggett. Leggett, the founder of The New York Gas Light Company, was granted the first franchise to lay underground gas pipes in New York City, and his home was the first house in New York to be lit by gas lights. John Murray, Jr., known for his benevolence and as one of the founders of the Free School Society and The Society for the Manumission of Slaves, is buried here. A number of families prominent in Long Island history have plots here, including the Hicks, Farrington and Lawrence families.

When the graveyard was closed at the end of the 19th century, Flushing Meeting bought one of the original plots at the Flushing Cemetery on 46th Avenue, and since that time Flushing Meeting members may be buried there.