He was a lieutenant de vaisseau on board the Géographe, a vessel whose officers also included an ensign (aspirant) called Charles Baudin.
François-André Baudin fell ill and was left behind on île de France in April 1801.
In November 1809, Baudin was ordered to take the 80-gun ships of the line Robuste and Borée, the 74-gun Lion and the frigates Pauline and Pomone and escort a twenty-ship convoy from Toulon to Barcelona to supply French troops fighting in the Peninsular War.
Seeing that the British had gained speed and was trying to block their path, Baudin ordered his ships to make for land as fast as possible, but this only led to the Robuste and Lion going aground – to deny them to the British, Baudin ordered them set on fire and scuttled near Frontignan.
Captain Senèz, commanding the Borée, stayed further offshore whilst still obeying Boudin's orders – he passed through the middle of the British squadron and escaped into the port of Sète, normally too small for ships of the line.