The creation of the Banovina of Croatia was Prince Paul's attempt to address the 'Croatian question' On 7 December 1937, Bauer died, and though still below the age of forty, Stepinac succeeded him as Archbishop of Zagreb. Presaging the Ustaše reign of terror during, Stepinac addressed a group of university students during in 1938, saying, 'Love for one's own nation must not turn a man into a wild animal, which destroys everything and calls for reprisal, but it must enrich him, so that his own nation respects and loves other nations.' In 1938, the before the outbreak of war. Stepinac voted for Maček's opposition list, while spread the false information that he had voted for 's. In the latter half of 1938, Stepinac had an operation for acute appendicitis.

In 1940, Stepinac received the regent at as he arrived in Zagreb to garner support for the 1939, which had created the autonomous within Yugoslavia. The Agreement was intended to address the 'Croatian question', but did not satisfy those demanding full independence. Pope declared the period from 29 June 1940 to 29 June 1941 as a year to celebrate 1300 years of Christianity among the Croats. In 1940, the celebrated 700 years in Croatia and the order's came to Zagreb for the event. During his visit, Stepinac joined the, on 29 September 1940. After the death of Bauer, Stepinac attempted to remain aloof from politics, and tried to unify Croatian Catholic organisations and subordinate them directly to his authority.

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He was unable to achieve this, probably because he was young and relatively inexperienced, and did not command the level of respect and authority usually accorded an Archbishop of Zagreb. The historian Mark Biondich observes that the Catholic Church had historically been on the fringes of Croatian mass politics and public life, and that the influence of the Church had been further eroded during the due to the royal dictatorship and the popularity of the anti-clerical HSS. Political and religious views [ ]. Zagreb Cathedral During his period as coadjutor archbishop and as Archbishop of Zagreb up to the -led in April 1941, Stepinac made his views clear on a number of political and religious issues. Foremost among these statements were those regarding,,.

Stepinac criticized Protestantism, stating in a speech in 1938 that 'the Catholic Church was the greatest civilising force in human history', but railed against those that wanted to deprive the Catholic Church of any influence in public life. He referred to the as the 'Deformation', and denounced as a false prophet who 'demolished the principles of legal authority given by the Lord'.

He went on to blame Protestantism for the 'hell in which human society suffers today', and said that it had opened the road to 'anarchy in all forms of human life.' Stepinac was also highly critical of Eastern orthodoxy, seeing it as a serious danger to both the Catholic Church and Croats in general. The day after the of 27 March 1941, he wrote in his diary: All in all, Croats and Serbs are two worlds, the north and south poles, which will never become close except by a miracle of God. The is the greatest curse of Europe, almost greater than Protestantism. In it there is no morality, no principle, no truth, no justice, no honesty. On the same day he issued an encyclical to his clergy, calling on them to pray for the young king, and that Croatia and Yugoslavia would be 'spared the horrors of war'.

This was consistent with long-standing practice of the Catholic Church to show loyalty to the state and its leadership. Stepinac was well aware of the fact that an estimated 200,000 mostly Croatian Catholics had converted to the Serbian Orthodox Church in the interwar period. He later claimed that Catholics were forced to convert to Orthodoxy during the period between the wars, but according to the historian, the principal reason for their conversions was the pro-Serb public policy in the Serb-dominated Yugoslav state meant that it was advantageous both politically and for career prospects to be a member of the dominant religion. Stepinac viewed the Yugoslav state as essentially anti-Catholic, particularly after the failure of the Yugoslav government to ratify the with the Vatican, which would have put the Catholic Church on a more equal footing with the Orthodox Church. He was also sensitive to the fact that the Concordat had been vetoed in the Yugoslav parliament partly due to pressure exerted by the Serbian church. In 1940, Stepinac had told Prince Paul: The most ideal thing would be for the Serbs to return to the faith of their fathers, that is, to bow the head before Christ's representative, the Holy Father.