Despite being a member of the Democratic Party, Clayton disagreed with President Franklin D. Roosevelt's New Deal agricultural policies. However, he supported FDR in the 1936 election because of the New Deal's free trade policies. When Clayton returned to government work in 1940, he worked for the Reconstruction Finance Corporation. He then worked to acquire strategic materials for the U.S. in an effort to keep them out of Germany's hands. This work was done as part of the Export-Import bank.