He was born in Hayingen in Lorraine. Upon the outbreak of the French Revolution, Molitor joined the French revolutionary armies as a captain in a battalion of militia. In 1793 he was given command of a brigade and served under Hoche under whom he fought at Kaiserslautern and Wissembourg. In 1795, Molitor was severely wounded in the Battle of Mainz. In 1799, Molitor was sent to Switzerland where he fought under André Masséna against an Austro-Russian force led by Alexander Suvorov. In 1800, he fought in the "Army of the Rhine" under Moreau.