Bayerlein served as a staff officer of General Heinz Guderian for the invasion of Poland and the Battle of France.

In Operation Barbarossa, the invasion of the Soviet Union, during June 1941, Bayerlein was assigned to Guderian's Panzer Group 2 staff.

When Rommel left Tunisia in March 1943 after the failed attack during the Battle of Medenine (Operation Capri), Bayerlein was appointed German liaison officer under the new commander, Italian Giovanni Messe.

The remnants of the Panzer Lehr Division slipped out of the Falaise pocket and moved east toward Vire in August 1944.

During this time, he and many other generals in Allied captivity wrote the European battle histories for the U.S. Army Historical Division.