After being appointed Pope, Lenny Belardo must navigate the political hallways of Vatican City. However, the new Pope shocks the Vatican with his desire to reject both publicity and the liberal philosophy of his predecessor. As a new type of awkward arrives to the Vatican in dreams and reality, the staff is facing personal and systemic critiques.

Lenny shocks the world with his first address, in which he demands Catholics worldwide devote themselves body and soul to God no matter the consequences. Sister Mary and Cardinal Voiello struggle to control Lenny, who admits that his conservative religious views were caused due to his parents abandoning him to an Italian orphanage to continue a hedonistic lifestyle.

With his first address, the young Pope Pius XIII, enraged the faithful present at the St. Peter's Square. The Vatican is now trying to limit the damage. Lenny agrees to a press conference, making his counselor Sister Mary read a short statement. Now Cardinal Voiello wants to put the pope under all restrictions.

Cardinal Voiello urges the young Pope Pius XIII to finally deal with the abuse scandal surrounding American Cardinal Kurtwell. The Pope shocks Voiello by requesting to remove all homosexuals from the Catholic Church without regard to the person. Voiello then tries to force Esther, the wife of a Swiss guardsman, to seduce the pope.

Voiello catches Pius in a compromising situation but hesitates to use the evidence against the Young Pope. More is revealed about Lenny's troubled past as he and Dussolier reconnect while running away from Sister Mary again. Gutierrez is assigned to an uncomfortable appointment in America. Upon the return of a famous papal headdress to the Vatican, Pius is finally prepared to deliver his opaque and rigid address to the Cardinals.

Nine months into Lenny's papacy, he gives his first audience to the Italian prime minister. Dussolier carries out a controversial edict.

Pius's opposition consolidates against him as his plan for a conservative revolution in the church continues to alienate the public. Sister Mary commits herself to deception. In the wake of a tragedy, Dussollier blames himself and decides to return to his mission in Honduras.

Pius struggles with emotional fallout from Dussolier's passing. Admist feminist protests, author Elmore Coen visits Pius for a conversation about sex. Spencer offers Pius spiritual guidance for handling his increasing guilt. Hoping to find clarity in his Papacy, Pius follows Sophia's suggestion to visit an African mission where he discovers moral ambiguity. Meanwhile, Pius's relation with the public grows more contentious as reporters begin digging into his past.

Gutierrez grapples with his alcoholism while investigating the crimes of Archbishop Kurtwell. As Spencer's condition worsens, Lenny opens up about the mysteries of his past. Meanwhile, Kurtwell attempts to retaliate against Pius by leaking unsent love letters to the press.

The Young Pope makes travel plans to Guatemala, to change them last minute, to "find God" in Venice, Everything changes and the finale remains open.