With the takeover of Austria and the Sudetenland successfully completed before the end of 1938, Toepfer busied himself with subversion in Alsace-Lorraine and elsewhere. He ran this operation using money parked in Liechtenstein, with a board headquartered in Basle, Switzerland, and a foundation based at Freiburg-im-Breisgau, in close reach of Alsace-Lorraine.

By this time, Toepfer's younger brother Ernst was living in Switzerland, having previously gained US citizenship after spending several years running a New York branch of the business. This made it easier to transfer money across international borders. Ernst Toepfer (who was to die of natural causes in 1941) had been secretary of the pro-Nazi "Wehrwolf" organisation in New York City in the late 1920s. In the 1930s, he had acted (he later claimed) as chauffeur and bodyguard for Sepp Schuster, leader of the New York City Nazis. The Toepfer brothers' main agent in Switzerland was Eugen Wildi, a lawyer and member of the Swiss fascist "National Front" who had transmitted Nazi funds to Alsace-Lorraine since the 1920s.

Meanwhile, on the French side of the border, the security services were observing the Toepfers' grantees. On 28 April 1939, a senior official in the Bas-Rhin department identified two Toepfer board members, Danish pastor Johannes Schmidt-Wodder and Wildi, as "very active agents of the German special services".

The French had good reason for concern. Toepfer board member Hermann Bickler headed an autonomist political party in Alsace. After the Nazis overran France, he became an SS colonel, Nazi Kreisleiter (district leader) in Strasbourg and then one of the heads of the Sicherheitsdienst (the SS intelligence service) in Paris. He headed the division responsible for protecting and promoting Nazi double agents within the French resistance. 

With the outbreak of war, Alfred Toepfer's obsession with deception made him a good candidate for the Abwehr (military intelligence). He was stationed mainly in Paris in a section responsible for subversion and sabotage. 

The war proved good for his business interests both within the Reich and in occupied Eastern Europe. His company opened branches in Poznan (Posen), Cracow (Krakow) and Lviv (Lemberg). It explored the commercial possibilities of the Caucasus until the military defeat at Stalingrad cut off this potential opportunity. Relatively little is known about the company's operations in occupied Poland. But it has been established that the Poznan office traded with the German administration of the Lodz ghetto, the country's second largest in the number of Jews cooped up within it.