Atfeh continued his role as chief of staff when the 1948 Arab–Israeli War broke out. Syrian troops suffered heavy losses during the first days of the war. Atfeh, along with Minister of Defense Ahmad al-Sharabati, were considered the principal parties responsible for the poor preparation and management of the war. Consequently, Atfeh was relieved from his duties soon after and replaced with then-Director of Public Security, Husni al-Za'im. In 1949, al-Za'im led a military coup that overthrew the al-Quwatli's government, and appointed Atfeh as his defense minister. Al-Za'im's rule lasted around five months, and in August 1949 Atfeh switched his allegiances again and supported the politicians that replaced him. After the 1949 elections Atfeh was appointed minister of defense by Syria's new president, Hashim al-Atassi. However, his term did not last long and he was relieved from his post after three months, after which he retired from public life.