Rubuta ci gaba don wannan sakin layi - A karkashin umarnin Madani, ya shiga kuma ya zama jagora a cikin yunkurin samun 'yancin kai na Indiya. Bayan Rarraba Indiya a 1947, Chowdhury ya goyi bayan ci gaban sabuwar Pakistan, yana aiki tare da jagorancin kungiyar Jamiat Ulema-e-Hind. Bayan da Bangladesh ta ayyana 'yancin kai
a shekarar 1971, ya yi kokarin hana aukuwar tashin hankali a kan mutane da sojojin Pakistan. Lokacin da sojoji suka kewaye 'yan uwansa hamsin a Ronokali, Chowdhury ya yi kira ga sojoji da su kare su. A wani lokaci kuma, ya sa baki ya ceci rayukan 'yan Hindu bakwai da suke cikin irin wannan yanayin. Chowdhury daga baya ya taka rawa a cikin kungiyar Khilafat ta Bangladesh, yana aiki a karkashin jagorancin Hafezzi Huzur kuma ya jagoranci yawancin taron ta.