Although al-Qawuqji and Grand Mufti al-Husseini had periods of considerable friction and discord, particularly during the 1936–39 Arab revolt in Palestine, the two men subsequently reached a rapprochement. Al-Qawuqji followed the Mufti from Lebanon to Iraq in October 1939, along with other members of the Mufti's entourage, including Jamal al-Husayni, Rafiq al-Tamimi, and Sheikh Hasan Salama. Al-Qawuqji became the Mufti's military advisor in the 'Arab Committee' that Haj Amin Husseini formed in Baghdad. Husseini's group, including, al-Qawuqji, played critical roles in the pro-Axis coup. His frequently demonstrated prowess won him fame among the Arab population and the esteem of Haj Amin Husseini. His popular following, however, was not altogether to the Mufti's liking. He was prominent in the Kingdom of Iraq during the Rashid Ali coup of 1941 and, during the subsequent Anglo-Iraqi War, he again fought against the British. Al-Qawuqji led approximately 500 "irregulars" in the area between Rutbah and Ramadi. He established a reputation as bold fighter. He was also known to either execute or mutilate his prisoners. After the Rashid Ali regime collapsed, al-Qawuqji and his irregular forces were targeted for destruction by the "Mercol" flying column and were chased out of Iraq. While still in Iraq, a British plane strafed and almost killed him.