The first Catholic presence in present-day Minnesota was that of Reverend Jean-Pierre Aulneau, a French missionary at Fort Saint Charles near Penasse He was killed by a Sioux war party in 1736.

[5] Peschges established the Confraternity of Christian Doctrine, a program of religious courses for rural youth, in the diocese and founded other organizations for agricultural development.

[1] After Peschges died in 1944, Pope Pius XII in 1945 appointed Monsignor Francis Schenk of Saint Paul to succeed him.

[1] He also founded summer boarding schools for children of the thousands of Mexican migrant workers who worked in the diocese.

[12] Following a Vatican investigation of Hoeppener for coercing a sexual abuse victim, Pope Francis ordered his resignation as the bishop of Crookston.

[15] In 2006, a teenage girl accused Reverend Joseph Palanivel Jeyapaul of raping and sodomizing her on many occasions in Greenbush when she was age 14 in 2004 and 2005.

[19] In 2011, Ronald Vasek, a former diaconate candidate, reported to the diocese that Reverend Roger Grundhaus had sexually abused him when he was a teenager during a trip to Ohio in 1971.

[23][24] In September 2019, on the direction of the Vatican, Archbishop Bernard Hebda of St. Paul and Minneapolis announced that he would investigate Hoeppner's actions.

This was the first investigation of an American bishop for failing to the follow the sexual abuse procedures in the 2019 papal document Vos estis lux mundi.

In July 2019, the diocese announced a $5 million legal settlement with 15 alleged victims of sexual abuse by diocesan clergy.