On the outbreak of the Second World War, Quirnheim was appointed a Staff Officer at the General Staff's organisational division.
He had initially welcomed Hitler's seizure of power, but began to distance himself from the new government as he became more aware of its brutality.
In 1941, for example, his support for the more humane treatment of civilians in Nazi-occupied Eastern Europe triggered a dispute between Alfred Rosenberg, the Reich Minister for the Occupied Eastern Territories, and Erich Koch, Reich Commissar for the Ukraine.

In 1942, while being promoted to lieutenant colonel and then to Head of Staff of the 24th Army Corps at the Eastern Front, Quirnheim strengthened his ties to the Resistance through his brother-in-law Wilhelm Dieckmann.
He was promoted to colonel in 1943, and the same year he married Hilde Baier.
On the outbreak of the Second World War, Quirnheim was appointed a Staff Officer at the General Staff's organisational division. He had initially welcomed Hitler's seizure of power, but began to distance himself from the new government as he became more aware of its brutality. In 1941, for example, his support for the more humane treatment of civilians in Nazi-occupied Eastern Europe triggered a dispute between Alfred Rosenberg, the Reich Minister for the Occupied Eastern Territories, and Erich Koch, Reich Commissar for the Ukraine.
In 1942, while being promoted to lieutenant colonel and then to Head of Staff of the 24th Army Corps at the Eastern Front, Quirnheim strengthened his ties to the Resistance through his brother-in-law Wilhelm Dieckmann. He was promoted to colonel in 1943, and the same year he married Hilde Baier.
Albrecht Mertz von Quirnheim