[2] In the late 1990s, he followed the recommendation of the Archbishop of Buenos Aires Jorge Bergoglio and declined an invitation to head a theological institute in Bogotá.

[2] He headed the Faculty of Theology at the Pontifical Catholic University of Argentina (CUA) when Cardinal Bergoglio nominated him to serve as its rector on 15 December 2009.

[4] Bergoglio resented this questioning of his judgment and Fernández found the process itself disrespectful when he traveled to Rome only to have the CDF cancel a meeting at the last minute.

[1] Pope Francis named him to the commission that drafted the concluding message (relatio) of the Extraordinary Synod of Bishops on the Family, held in October 2014.

[15] Pope Francis named him Archbishop of La Plata on 2 June 2018 to succeed Héctor Rubén Aguer,[7] who had been in poor health for several years, had submitted his resignation as required on his 75th birthday just a week earlier, and was long identified as an opponent of Bergoglio within the Argentine Episcopal Conference.

[17] As archbishop in 2019, he is accused of supporting a La Plata priest Father Eduardo Lorenzo in the face of five sex abuse allegations.

[18] [19] On 1 July 2023, Pope Francis appointed him to succeed Cardinal Luis Ladaria Ferrer as prefect of the Dicastery for the Doctrine of the Faith (DDF) in mid-September.

[21] A "highly unusual"[22] letter written in Spanish[23] from Pope Francis to Fernández was published alongside the announcement of his appointment.

In their statement SNAP and ECA said that in their view, by tapping Fernández to lead the DDF, “Pope Francis demonstrates not only poor judgment, but also gross disrespect to Catholic victims around the world.”[29] On 18 December 2023 Pope Francis, approved a DDF ruling, allowing priests to bless unmarried and same-sex couples.

On 8 April 2024, Pope Francis, approved the declaration, Dignitas Infinita, which condemned violations of human dignity, including, gender theory, as well as: abortion and discrimination against women.

His relationship with Pope Francis dates to his work for the Argentine Bishops' Conference where he demonstrated his ability to incorporate different viewpoints in drafting group statements.

The book resurfaced in 2023 following Fernandez's appointment to the DDF; he defended it, denying that it contained heresy or heterodox teachings, but stated that he would not write it today and that its republishing had already been discontinued.

Fernández's description of "an experience of love, a passionate encounter with Jesus, that a sixteen-year-old-teenager [girl] told me about", is in the book's sixth chapter.

Dove vuole portare la Chiesa (The Francis Project: Where He Wants to Take the Church), a book-length interview Fernandez gave to the journalist Paolo Rodari from the Italian daily La Repubblica, he describes the broad themes of Francis' papacy, the need to view moral issues in context rather than assert them as non-negotiable, to "set hearts on fire" rather than reiterate dated "philosophical or natural law-related" arguments.