Later that year he was appointed as a chief of staff of the Albanian government brigade fighting against Serb forces in the Martanesh area.

In December 1924, when Ahmet Zogu returned to Albania supported by Yugoslav forces, he fought against him in the Battle of Tujan.

Admitting his excellent capacities Zogu reintegrated Spiro Moisiu in the Albanian governmental forces.

During 1937–1938 he again achieved excellent results at military school in Tirana in studies for senior officers and graduated as major.

Accepting an invitation for his reinstatement into the Albanian governmental forces, Moisiu returned to Albania and at the end of 1940, while serving as the commander of Tomorri battalion, he was sent to the Italian-Greek front.

He was there contacted by communists who in July 1943 proposed him to be the General Commander of Communist-dominated Albanian National Liberation Army (ANLA).

Under his military leadership the ANLA was able to withstand two major offensives of the Germans in the winter of 1943-44 and in June 1944, while at the same time keeping the Germans under constant attacks; to win the war against the nationalist forces who opposed the ANLA, such as Balli Kombëtar, Legaliteti and others; and to liberate the country on November 29, 1944, Albania being the only country in Europe to have done so without the participation of Allied forces.