According to Albanian sources he studied at the local Rüştiye, then in Yannina, before going to the today's Faculty of Political Science, Ankara University ("Mekteb-i Mülkiye") which he finished in 1910.

According to Turkish author Çankaya, he studied at the local school in Elbasan, then in Mercan idadisi in Istanbul before entering the Mülkiye.

[3] As a student in the Ottoman capital he joined the Revolutionary League ("Cemiyet-i İnkılabiye") against the autocracy of Sultan Abdul Hamid II.

After the Young Turk Revolution he worked for supporting the Albanian language at the Mülkiye, and posted articles in the liberal press against the Committee of Union and Progress using the signature "Asim Cenan".

According to Sejfi Vllamasi's (1883–1975) memories, there Kruja would be the main opponent of the Congress of Lushnjë event together with Fejzi Alizoti, Myfit Libohova, and Sami Vrioni.

In 1922, he was involved in a coup d'état attempt against the government of Xhafer Ypi together with the north-east Dibra clan of Cen Elezi and Elez Isufi, and had to temporarily flee from Albania to Yugoslavia.

He is remembered for the public speech held on December 24, 1942, in response of the Anthony Eden's statement in accordance with the communique of the Greek government in London (in exile) which stated that Britain and US would not recognize any border changes established by the Fascists, and that neighboring countries would have the right to claim parts of Albania at the end of the war.

[5] Following the Axis occupation of Yugoslavia (in which Kosovo was occupied by Albania), the Albanian authorities under Mustafa Kruja forcibly expelled 70,000–100,000 Serbs, primarily colonists.

[6] Fascist Italy colonized Kosovo and Macedonia with 70,000 Albanians, who carried out religious persecution in the form of damaging and confiscating churches and monasteries, and exilement and murder of Orthodox priests.