In 1806 Thomières joined the staff of Marshal Jean Lannes and served in Prussia and Poland. He received promotion to general officer in July 1807. He participated in the 1807 invasion of Portugal. On 20 August 1808 he was wounded while leading his brigade at Vimeiro. He led a brigade at Corunna, Bussaco, and Fuentes de Onoro before being appointed to head a division. Thomières is one of the names inscribed under the Arc de Triomphe on Column 38.