Ali Shkupi was not active during World War II, although he was an opponent of the Italian invasion, as well as the German one. The Nazis would burn his house in Tirana. After the war, he resettled in Shkodër. He died on 3 December 1953 and was buried in Shkoder. He was reburied in Tirana in the '80s. In 1992, Ali Shefqet Shkupi was decorated for "Patriotic Activity of First Class" by the Albanian government.