When the Ba'ath Party gained power in the 1963 coup, Atrash became Minister of Social Affairs and in 1965 the head of the Revolutionary Command Council (RCC). A second coup by left-wing Ba'athist officers resulted in a split within the party between the coup officers led by the Military Committee and the founders led by Michel Aflaq, with Atrash being an ardent supporter of the latter. He was subsequently imprisoned, but released in the aftermath of Syria's defeat in the 1967 War with Israel. After two years of self-imposed exile in Lebanon, he returned to Syria where he mostly abandoned political life. He died on 14 November 2006 and was buried near his hometown of al-Qurayya.