In January 1945 he was appointed governor ("chao khoueng") of Houaphan where he remained until the Japanese surrender in August 1945.

The following month, Phoumi cooperated with Free French forces when they briefly seized the town of Sam Neua, but subsequently he joined the anti-colonialist Lao Issara movement and worked closely with the Viet Minh to oppose the return of French authority in Indochina.

The Resistance government gained no international recognition, but Phoumi nominally retained both positions until the Geneva Agreements of 1954 brought the First Indochina War to an end.

In March 1955, Phoumi was one of the founding members of the Lao People's Party and was elected to its Political Bureau (Politburo).

After the Battle of Vientiane in December 1960 and the subsequent retreat of Neutralist forces to the Plain of Jars, Phoumi was instrumental in arranging for Pathet Lao-Neutralist collaboration.

For the next ten years, Phoumi alternated between living in the limestone caverns of Viengxay and leading various Pathet Lao delegations to international communist gatherings.