York returned to St. Louis in early 1809, but Clark still viewed him unfavorably. "He is here but of verry little Service to me," Clark wrote to Jonathan. "[York is] insolent and Sulky, I gave him a Severe trouncing the other Day and he has much mended Sence."
The last mention of York in William Clark's letters appears in August 1809; Clark was so displeased with him that he determined to hire him out or sell him. John O'Fallon, Clark's nephew, wrote in 1811: "The term for which [York] was hired to Mr. Young yesterday expired but I believe agreable to request Mr. Fitzhugh has again hired him to a Mr. Mitchell living about seven miles from this place.... I apprehend that he has been indifferently clothed if at all by Young...." O'Fallon further notes that York's wife had moved with her master and the rest of his household to Mississippi; it is unlikely that York and his wife saw each other again. Ten years after the expedition's end, York was still enslaved, working as a wagoner for the Clark family.
In 1832, writer Washington Irving interviewed Clark and asked of York's fate. Clark replied that he had finally freed York and said, astonishingly, that his former slave wasn't happy with his freedom and tried to return to Clark—dying of cholera along the way.
But did he? In 1832, fur trader Zenas Leonard, visiting a Crow village in north-central Wyoming, "found a Negro man, who informed us that he first came to this country with Lewis and Clark—with whom he also returned to the state of Missouri, and in a few years returned again with a Mr. Mackinney, a trader on the Missouri river, and has remained here ever since—which is about ten or twelve years."
On January 17, 2001, President Clinton promoted York posthumously to the rank of honorary sergeant, Regular Army.