In 1922, he shocked the clergy and his family when he gave up all talk of a career and entered the Basilian Order, which had begun a major reform of its life and work. He entered the Saint Nicholas monastery in Mukachevo in the humble roles of being a postulant and then a novice, just as any beginner in the ascetical life would. He wrote to his parents that he most definitely did not want the episcopal rank or the office of a Canon, as he saw himself as being unworthy. He was given the name Paul in 1923 as a professed monk; he now bore the names of the two great apostles.
On March 25, the feast of the Annunciation, he was consecrated bishop in Saint Clement Basilica in Rome and Pope Pius XI received the young bishop in an audience in which he exhorted Bishop Gojdič to stand firm, prophetically telling him, "do not hesitate, if need be, to shed your own blood in defense of the Holy Union." In yet another symbolic moment, the pope presented Bishop Gojdič with a metal cross to wear, as a sign "of all those heavy crosses that the good Lord will deign to place upon your shoulders." The bishop wore that cross until his arrest in 1950 and often meditated on that prediction while he was in prison.
Czechoslovakia was much more religious than Bohemia, with a vibrant Catholic Church, both Greek and Latin, along with strong Lutheran and Reformed Churches, and religious Jews. Father Andrej Hlinka founded the Slovak People's Party which carried 40% of the Slovak vote. Priests were active in the party, which called for greater autonomy for Slovakia and an end to Prague’s anti-Catholic attitudes. The slogan "One God, One People, One Party" reflected Roman Catholic beliefs mixed with a worsening authoritarian trend after the Munich Crisis of 1938 which destroyed the Czechoslovakian state. A radical, anti-Jewish wing began looking to Nazis in Germany despite Nazi persecution of the Catholic Church and Pope Pius XI's fierce condemnation of the Nazis in 1937. Father Josef Tiso became the leader of both the HLS'S and Slovakia.
Violent attacks against him took place in the press and radio, accusing him of espionage and treason. When a false sobor (council) was forcibly attended by clergy and laity on April 28, 1950, a mob of Orthodox collaborators went to the cathedral, broke open the doors and stormed inside. Gojdič was arrested on charges of “opposing the will of the people.” He was offered money and the post of “patriarch” of the Orthodox Church of Czechoslovakia. To all of it he replied quite bluntly, "I am already 62 years old, and I am sacrificing all my property and residence, but I will not betray my faith under any circumstances, because I want my soul to be saved."