In 1945 he was among the founders of the CSU. He was engaged in continuous strife with the party leader, Josef Müller over party politics. Müller wished to make the party multi-confessional, while Schäffer tried to move it towards a revival of the Catholic-dominated BVP. He was made the first postwar prime minister of Bavaria by General George S. Patton in 1945, but was relieved of his post by General Dwight D. Eisenhower after a couple of months, when his anti-Semitic past became known. Eisenhower, unlike Patton, also disliked the fact that Schäffer hired ex-Nazis for his administration. He was barred from politics by the US authorities until 1948, accused of being a Nazi sympathizer. He managed to clear himself of this charge and reentered politics afterwards.