The newly promoted Field Marshal Rupprecht clashed often with Moltke's replacement, Erich von Falkenhayn, and later became a bitter enemy of Ludendorff's due to their differences over ultimate war objectives. The Bavarian Crown Prince recognized the need to bring the conflict to a close many months before his superiors at Supreme Command came to the same conclusion; but as his armies engaged the Allies on the Scheldt and Lys rivers in the fall of 1918, he still expected that "the Prussians would fight on to the last Bavarian."

After the war, Rupprecht lived in Austria with his only surviving son Albert. When his mother Maria Therese died in 1919, he succeeded to all of her British rights and was thereafter recognized by the Jacobites as "King Robert I and IV" although they generally referred to him as "King Rupert". He then moved back to Germany, living in his castle at Berchtesgaden and marrying his second wife, Princess Antonia of Luxembourg, who happened to be the first cousin of his first wife Marie Gabriele. When his father died in 1921, many Bavarians recognized Rupprecht as their king.

During the Nazis' initial push for power, one of the main reasons Rupprecht declined participation in Hitler's Beer Hall Putsch was
because of the presence of Ludendorff, whose violent attacks on Catholicism repulsed him. His opposition to the Nazi Party forced him to seek asylum in Italy during the late 1930's. Although he remained in Florence throughout the Second World War, successfully evading capture by the Nazis in 1944, his wife and children were actually imprisoned in Nazi concentration camps. He traveled the world wide, publishing many books about his adventures, and he also acquired a noteworthy art collection over the years. Crown Prince (King?) Rupprecht died at Leutstetten Castle in August 1955 and was interred at the Theatiner Church in Munich. At his funeral, the royal crown and Bavarian scepter were withdrawn from the State Museum and placed upon his coffin.