During the post-Civil War Reconstruction era, Cowan found himself increasingly in line with the policies of Andrew Johnson, which earned him the displeasure of the Radical Republicans who controlled the Senate and the Republican Party in Pennsylvania. Cowan was a candidate for reelection with the support of Democrats in the Pennsylvania legislature, but lost to former ally Simon Cameron. Johnson then nominated Cowan to be U.S. Minister to Austria, but Cowan's Radical Republican opponents in the Senate tabled the nomination, so it was never acted on.