The Pilgrims were Separatists - English Protestants who had concluded that the Church of England was unreformable and that the only path to a true church was to leave it entirely. This was illegal. In 1607 a small congregation in Scrooby, Nottinghamshire, attempted to emigrate to the Netherlands. They were arrested and turned back at the coast. They tried again, in pieces, the following year. By 1608 they had reached Amsterdam. The Dutch Republic was the most religiously tolerant country in Europe - not perfect, but vastly better than Stuart England - and Leiden, with its young university and its booming cloth industry, was where many of them eventually settled in 1609.

Leiden in 1609 was a city of about forty thousand people, growing fast on the wool trade. The Pilgrims integrated into the working class. William Bradford, who would later govern Plymouth Colony, learned to weave fustian - a coarse cotton-linen blend used for cheap clothing. William Brewster ran an underground English-language print shop in a back alley off the Pieterskerk, publishing religious texts that Stuart agents tried unsuccessfully to suppress. Their pastor John Robinson held meetings in a house called the Groene Poort, the Green Gate, across from the Pieterskerk. Children were born; weddings were celebrated; some families prospered and others struggled. The Dutch tolerated them, and the Pilgrims tolerated the Dutch back. But the longer they stayed, the more their children sounded Dutch, and the more the parents worried about losing their English identity entirely - which was, in part, why they began looking westward.

In the summer of 1620 about half the Leiden congregation - the most adventurous half, mostly the younger families - sold what they owned and boarded a canal boat for Delfshaven. There they joined the Speedwell, a small ship that took them across the Channel to Southampton. The Speedwell turned out to leak badly. The plan to sail two ships across the Atlantic collapsed. The leaky vessel was sold, the passengers consolidated onto the Mayflower, and 102 souls set out in September - a dangerously late departure for an Atlantic crossing. They reached Cape Cod after a brutal sixty-six-day voyage. Their first harvest the following autumn, shared with the Wampanoag people whose land they had landed on, became the origin story of the American Thanksgiving. Many of them died that first winter. William Bradford's wife Dorothy drowned in Provincetown harbor before they ever made landfall on the mainland.

Jeremy Bangs, an American historian who had married a Dutch woman and settled in Leiden, founded the museum in 1997. He housed it in a building that dated to the 1360s and 1370s, at Beschuitsteeg 9, right next to the bell tower of the Hooglandse Kerk. The building was almost certainly standing when the Pilgrims walked past it in 1620. Bangs assembled a collection of period furniture, books, sixteenth- and seventeenth-century maps by Mercator, engravings by Adriaen van de Venne, and household objects from Pilgrim Leiden and Plymouth Colony. He published, almost single-handedly, more new scholarship on the Leiden years than had appeared in the previous century combined. In October 2025, the museum moved a few streets away to Kloksteeg 16a, now operated by the Stichting Pieterskerk Leiden, the foundation that runs the church where John Robinson is buried.

The story Americans hear in elementary school is a story about a ship, a rock, and a feast. The Leiden museum tells a longer and more complicated story. The Pilgrims left because they did not feel at home in Holland, which welcomed them. They sailed to a continent they did not own, where the people who lived there fed them through a winter that should have killed all of them. Their leader is buried in a Dutch church, not in Massachusetts. The Vrouwekerk where some of them worshipped is now ruins; the museum coordinated the installation of a bronze memorial there in 2011, commemorating the Pilgrims and the early Dutch colonists of New Netherland in the same plaque. Two paths out of Leiden, two colonial origin stories, one bronze. It is a more accurate Thanksgiving than the picture-book version.