[6] During the planning of Operation Barbarossa, General Thomas' pragmatic and realistic nature once again gripped him as he thought a full-scale war with the Soviet Union should be delayed until the logistical concerns were remedied.

Thomas informed Colonel-General Franz Halder, the Chief of the OKH General Staff, that the attack on the Soviet Union would experience logistical delays due to the fact that Russian railways were of a different gauge than German ones.

The Chief of the Operations Staff for the OKW, Colonel-General Alfred Jodl, submitted the report to Hitler but he became irate when the estimates were given to him, mentioning Thomas, who "rated the Soviet war potential as high".

Through contacts with his former superior Ludwig Beck, Carl Friedrich Goerdeler and Johannes Popitz, he got to work as early as 1938–1939 on the planning for a military coup d'état against Adolf Hitler.

[12] Thomas has been described as someone who at times "toyed with opposition to Hitler's war" but who fundamentally was a "ruthless pragmatist" whose only concern was "Germany's future as a great power".

[13] He was deeply involved in the making of Nazi policy for the occupied Soviet Union, which was to exploit the resources of the country for the benefit of Germany and the German armed forces, at the expense of the deaths by starvation of millions of people.

An internal Wehrmacht memorandum prepared by his staff described this policy and acknowledged that "if we take what we need out of the country, there can be no doubt that many millions of people will die of starvation".

In far more unvarnished language than was ever used in relation to the Jewish question, all of the major agencies of the German state agreed to a programme of mass murder, which dwarfed that which Heydrich was to propose to the Wannsee meeting nine months later.

[2]The historian, Christopher Browning, wrote that on 2 May 1941, the state secretaries of various ministries met with Thomas and agreed to make it a priority to supply the army with food from Russia and to ship other essential agricultural products, including grain, to Germany.