After the Germans invaded Poland in 1939, he joined the Polish Army as an officer and took part in the defence of Poland against the invasion. He later explained to the Australian novelist Thomas Keneally how he was wounded on the San River where his life was saved by his sergeant major, who carried him to a field hospital. After Poland was defeated and partitioned between Nazi Germany and the Soviet Union, Pfefferberg needed to decide whether it would be safer to travel east towards the Soviets or west towards the Germans. He later recalled this choice: