In 1803-04, he helped to supply the Lewis and Clark Expedition, though neither explorer particularly liked him. After the expedition returned to St. Louis, Lisa organized the first large-scale fur trading and trapping venture an in 1807, with partners, Pierre Menard, William Morrison and about 50-60 trappers, loaded in keelboats, made his first expedition up the Missouri River. After meeting opposition from the Arikara, Mandan and Assiniboine Indians, the party reached the confluence of the Yellowstone and Big Horn Rivers in present-day Montana, and soon built Fort Raymond.

After thoroughly working the area and obtaining thousands of pelts, they returned to St. Louis. He then formed the St. Louis Missouri Fur Company in the winter of 1808-09 along with several partners including Pierre Choteau, Sr., Auguste Choeau, Jr., Andrew Henry, Pierre Menard, Benjamin Wilkinson, Reuben Lewis, William Clark, Sylvestre Labbadie, and William Morrison.

In the spring of 1810, Andrew Henry and Pierre Menard, led by John Colter, left Fort Raymond with a group of trappers, traveling to the Three Forks of Montana, where they established Fort Henry. They then crossed over Bannock Pass into present-day Idaho, where they established a second post on Henry's Fork of the Snake River, which was also called Fort Henry. However, both forts were short-lived, as the post at the Three Forks was abandoned after only a few months due to continuous attacks by Blackfoot warriors. Fort Henry in Idaho was abandoned the following year.

The War of 1812 created difficulties for the St. Louis Fur Company and they were forced out of the dangerous Dakota country. The partnership was dissolved the same year. Spending more time on other business venture, he took part in forming the first bank in St. Louis - the Bank of St. Louis in 1813 and was named one of the commissioners.

Lisa’s wife, Mary died in 1817, while he was living among the Omaha Indians. He soon took an Indian wife named Mitain and the couple would have two children. However, while still married to Mitain, he married a St. Louis widow named Mary Hempstead Keeney on August 8, 1818.