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After the collapse of the French monarchy, André Michaux, who was a royal botanist, lost his source of income. He actively lobbied the American Philosophical Society to support his next exploration. His efforts paid off and, in early 1793, Thomas Jefferson asked him to undertake an expedition of westward exploration, similar to the Lewis and Clark Expedition, the Corps of Discovery, conducted by Meriwether Lewis and William Clark a decade later. At the time of the planned Michaux expedition, Lewis was an 18-year-old protégé of Jefferson who asked to be included in the expedition, and was turned down by Jefferson.

Before Michaux set out, however, he volunteered to assist the French Minister to America, Edmond-Charles Genet. Genet was engaging in war-like acts against English and Spanish naval interests, aggravating relations between America, England and Spain. George Rogers Clark offered to organize and lead a militia to take over Louisiana territory from the Spanish. Michaux's mission was to evaluate Clark's plan and coordinate between Clark's actions and Genet's. Michaux went to Kentucky, but, without adequate funds, Clark was unable to raise the militia and the plan eventually folded. It is not true, as sometimes reported, that Thomas Jefferson ordered Michaux to leave the United States after he learned of his involvement with Genet. Though Jefferson did not support Genet's actions, he was aware of Genet's instructions for Michaux and even provided Michaux with letters of introduction to the Governor of Kentucky.^[7]

On his return to France in 1796 he was shipwrecked, however most of his specimens survived. His two American gardens declined. Saunier, his salary unpaid, cultivated potatoes and hay and paid taxes on the New Jersey property, which is now still remembered as "The Frenchman's Garden", part of Machpelah Cemetery in North Bergen.