Under Madani's instructions, he took part and became a leader in the Indian independence movement. Following the Partition of India in 1947, Chowdhury supported the development of the newly created Pakistan, working alongside the leadership of the Jamiat Ulema-e-Hind organisation. After Bangladesh declared independence in 1971, he attempted to prevent incidents of violence against people by the Pakistani military. When fifty of his relatives in Ronokali were cornered by the army, Chowdhury successfully appealed to the soldiers to spare them. On another occasion, he was able to intervene to save the lives of seven Hindus under similar circumstances. Chowdhury subsequently played an active part in the Bangladesh Khilafat movement, working under the leadership of Hafezzi Huzur and presiding over many of its conferences.