In 1804, Wilkinson received 12,000 pesos from the Spanish for information on American boundary plans.[243] Wilkinson also received advances on his salary and payments on claims submitted to Secretary of War Henry Dearborn. This damaging information apparently was unknown to Jefferson. In 1805, Jefferson trusted Wilkinson and appointed him Louisiana Territory governor, admiring Wilkinson's work ethic. In January 1806, Jefferson received information from Kentucky U.S. Attorney Joseph Davies that Wilkinson was on the Spanish payroll. Jefferson took no action against Wilkinson, there being, at the time, a lack of evidence against Wilkinson.[244] An investigation by the House in December 1807 exonerated Wilkinson.[245] In 1808, a military court looked into Wilkinson but lacked evidence to charge Wilkinson. Jefferson retained Wilkinson in the Army and he was passed on by Jefferson to Jefferson's successor James Madison.[246] Evidence found in Spanish archives in the 20th century proved Wilkinson was, in fact, on the Spanish payroll.[243]

Foreign affairs (1805–1809)
Attempted annexation of Florida
In the aftermath of the Louisiana Purchase, Jefferson attempted to annex West Florida from Spain, a nation under the control of Emperor Napoleon and the French Empire after 1804. 