He returned to public life in December 1991 when he was appointed Minister of Defense in Vilson Ahmeti's technocratic government.

Moisiu's advice was to concentrate efforts on the reconstruction of the armed forces, which were in bad condition, and to start preparations for joining the North Atlantic Treaty Organisation (NATO).

On January 24, 1995, he signed an individual association treaty binding Albania with NATO's Partnership for Peace project.

In 2002, under pressure from international organizations, Moisiu was chosen by Sali Berisha and Fatos Nano as a consensus candidate for the presidency after the end of Rexhep Meidani's term.

Moisiu was elected by the People's Assembly by a vote of 97 to 19 (with 14 abstentions) and he was sworn in for a five-year term as president on July 24, 2002.

Moisiu promised to contribute to the strengthening of parliamentary democracy, the stabilization of the judiciary system and the integration of Albania into Euro-Atlantic structures.