In 1799, Molitor was sent to Switzerland where he fought under André Masséna against an Austro-Russian force led by Alexander Suvorov, particularly at the Klöntal and Näfels.

In 1807, Molitor was transferred to the German theatre of operations, where he served against the Swedes around Stralsund.

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.

Upon the return of the emperor from Elba, Molitor joined him during the Hundred Days, for which he was stripped of his functions after Napoleon's defeat.

After the July Revolution, Molitor was allowed to keep all his functions and he later served as Governor of Les Invalides and as Grand Chancellor of the Legion d'Honneur.