Upon France's defeat in 1940, Duclos, most senior PCF official in France, engaged in negotiations with the Nazi authorities with a view to legalising the Communist Party (banned following the signature of the Molotov-Ribbentrop Pact and the declaration of war) as well as requesting permission to restart publication of the PCF daily (l'Humanité) (banned by the French government for the same reasons). These negotiations did not succeed, heling to protect the PCF's post-war credibility among many members of the masses.
After 1950, Maurice Thorez's health faltered, but Duclos remained one of the most influential members of the Party. He was acting Secretary General from 1950 to 1953 in Thorez's absence and was instrumental in eliminating his rival André Marty from the Party's leadership. Waldeck Rochet's own failing health prompted Duclos to run as the Party's presidential candidate in the the 1969 election, scoring 21.27% of the vote, the highest ever for a Communist presidential candidate in France.