In his last years, Walden focused on history of chemistry and collected a unique library of over 10,000 volumes. The library and his house were destroyed when the British bombed Rostock in 1942. Walden moved to Berlin and then to Frankfurt am Main, where he became a visiting professor of the history of chemistry at the local university. He met the end of World War II in the French Occupation Zone, cut off from Rostock University, located in the Soviet Zone, and thus left without any source of income.
Walden survived on a modest pension arranged by German chemists, giving occasional lectures in Tübingen and writing memoirs. In 1949, he published his best-known book, History of Chemistry. He died in Gammertingen in 1957, at the age of 93. His memoirs were published only in 1974.