In 1980, when Yoweri Museveni went to the bush to wage the National Resistance War, Bidandi did not go with him, although he clandestinely offered assistance to NRA supporters who sought his help. When Museveni won that war, Bidandi worked with him in the new government as Minister of Local Government from 1989 until 2004. In 2004, he resigned from the Cabinet after disagreeing with Museveni over the latter's desire to run for a third term as President.