Molitor was promoted to the rank of "général de division" in 1801. He was sent with Massena to Italy in 1805, where he served at Vago and Caldiero. In 1806 he took part in the relief of Republic of Ragusa. In 1807, Molitor was transferred to the German theatre of operations, where he served against the Swedes around Stralsund. He was then made governor of Pommern and was granted a comital title by Napoleon. In 1809 he was given command of a division in Massena's IV Corps and he saw action in the battles of Aspern and Wagram. In 1810 he was sent to occupy the cities of the Hanseatic League, from 1811 to 1813 he served in Holland, in the campaign of 1814 he served under MacDonald.