Baur was appointed head of the Hitler's personal squadron, initially based at Oberwiesenfeld, Munich. As the Luftwaffe was not yet officially established, Hitler wanted Baur to be able to command sufficient power and respect to assure his security, therefore, Baur was commissioned a Standartenführer (colonel) in the Schutzstaffel (SS No. 171,865) by Heinrich Himmler in October, 1933.
Baur was given the task of expanding and organising Hitler's personal squadron and the government "flying group". In 1934, Baur was promoted to the rank of SS-Oberführer. Hitler allowed Baur to fill his squadron with experienced Luft Hansa pilots, including Georg Betz who became co-pilot for Hitler's aircraft and Hans Baur's substitute. By 1937, Hitler had three Ju 52 airplanes for flight use. Then in 1937, Hitler obtained a new aircraft, the Focke-Wulf Fw 200 Condor which was named, "Immelmann III". The Condor had a much greater range and was faster than the Ju 52. In 1942, an improved model of the Condor was put into use for Hitler's travels and Baur continued to be his primary pilot. A Ju 290 was assigned to Hitler's renamed squadron, Fliegerstaffel des Führers (FdF) in late 1944. Modifications were completed by February 1945 at the FdF's base at Pocking, Bavaria. Baur tested the aircraft, but Hitler never flew in it. Still by the end of the war, Baur commanded a total of 40 different aircraft, including Ju 52, Condors, Ju 290 and the little Fieseler Fi 156 Storch.
Although he tried to convert Baur to vegetarianism, Hitler also invited him to the Reich Chancellery for his favourite meal of pork and dumplings for his 40th birthday, and gave him a Mercedes Benz to replace his personal Ford.