A native of Zagreb, between December 1939 and April 1941, Magovac was the editor of HSS newspaper Seljački dom (Peasant Home) jointly with Juraj Krnjević, when the World War II invasion of Yugoslavia happened.

[1] In 1943, he moved to the territory held by Yugoslav Partisans and led a faction of the HSS cooperating with them against the Axis powers.

During the second session of the State Anti-fascist Council for the National Liberation of Croatia (Zemaljsko antifašističko vijeće narodnog oslobođenja Hrvatske, ZAVNOH) established and dominated by the Communist Party of Croatia (Komunistička partija Hrvatske, KPH) as the supreme representative body in Croatia, Magovac founded the HSS executive committee as the top governing body of the HSS in the national liberation movement.

[1] As a ZAVNOH delegate, Magovac was also appointed a member of the Anti-Fascist Council for the National Liberation of Yugoslavia (Antifašističko vijeće narodnog oslobođenja Jugoslavije, AVNOJ) led by the Communist Party of Yugoslavia (Komunistička partija Jugoslavije, KPJ).

[1] Soon afterwards, Magovac came into conflict with the KPH secretary Andrija Hebrang over independence of the HSS within the Partisan national liberation movement and his resistance to denounce HSS president Vladko Maček a traitor for his reluctance to support the Partisans and his passivity.