On February 2, 1977, Hubbard was appointed Bishop of Albany by Pope Paul VI. He received his episcopal consecration on March 27, 1977. He was the youngest bishop in the country at the time, and was dubbed "the boy bishop." Hubbard served as chairman of the U.S. Conference of Catholic Bishops Committee for International Justice and Peace and on the Subcommittees on the Catholic Campaign for Human Development and the Church in Africa. He also served on other national bishops’ committees, including the Committees on Human Values, Marriage and the Family, Communication, Laity and North American College. Hubbard was appointed by Pope John Paul II to the Vatican's Secretariat for Non-Christians. He is a supporter of the ecumenical movement, serving as Roman Catholic Co-chair of the Oriental Orthodox-Roman Catholic Consultation. Under his leadership as bishop, the Roman Catholic Diocese of Albany maintained an active Catholic-Jewish dialogue. During his tenure as bishop, Hubbard presided over a nearly $20 million renovation project at the Cathedral of the Immaculate Conception. He also led a parish consolidation process—known as "Called to BE Church"—that resulted in the closing of 33 parishes. Hubbard had a reputation as a liberal bishop. He is known for progressive views on drug addicts and prisoners, and for advocacy of sometimes unpopular social justice issues. He is also noted for his anti-poverty efforts. Upon becoming bishop, Hubbard sold a large house where previous bishops had lived in luxury with a domestic staff. He also dispensed with the custom of having a luxury car and a driver. In 1992, he began living "in almost monastic simplicity in a nondescript, squat brick building" across the street from the Cathedral of the Immaculate Conception. As of 2013, then-Bishop Hubbard reportedly collected an annual salary of $33,508, the same salary as any diocesan priest with a similar number of years of service. Hubbard once sued to prevent abortion clinics from opening in the cities of Albany and Hudson, and he headed New Yorkers Against the Death Penalty.
Abuse crisis and allegations
In February 2004, Hubbard was accused of having engaged in homosexual activity with two different men in the 1970s. Hubbard denied the accusations and asserted that he had never broken his vow of celibacy. At the request of the Diocese of Albany, the accusations against Hubbard were investigated by former U.S. Attorney Mary Jo White. In June 2004, White released a 200-page report stating that she had found no credible evidence to support the accusations against Hubbard. White added that the investigation found "no evidence that Hubbard 'led a homosexual lifestyle, engaged in homosexual relations or visited gay bars'". Furthermore, White indicated that her investigative team had reviewed more than 20,000 documents and conducted over 300 interviews in connection with the Hubbard investigation. Also in 2004, the Diocese of Albany reported that 19 priests had committed sexual abuse in the past 53 years, and that investigations were pending into allegations involving 10 current and former priests. On March 19, 2011, Hubbard placed three retired priests on administrative leave and removed another from the ministry after receiving allegations of child sexual abuse. Hubbard has apologized for shortcomings in the way that he and the Diocese responded to the sexual abuse crisis. In 2004, during Hubbard's tenure, the Diocese of Albany created the Independent Mediation Assistance Program; this program allowed persons who were abused by diocesan priests or employees as minors to request and obtain financial assistance. On August 14, 2019, a civil lawsuit was filed in which Hubbard was accused of sexually abusing a teenaged boy in the 1990s. On August 16, Hubbard responded, "'With full and complete confidence, I can say this allegation is false. I have never sexually abused anyone in my life. I have trust in the canonical and civil legal processes and believe my name will be cleared in due course.'" Hubbard also announced that he was taking a voluntary leave of absence from public ministry until the matter was resolved. On September 16, 2019, an unnamed woman alleged that Hubbard and two other priests had sexually abused her in the rectory of Immaculate Conception Church in Schenectady in the late 1970s when she was a teenager. Hubbard denied this accusation as well.
Retirement
Hubbard submitted his required letter of resignation to Pope Francis on October 31, 2013, when he reached the age of 75. On February 11, 2014, the Vatican announced that Pope Francis had accepted Hubbard's resignation and appointed as his successor Rev. Msgr. Edward Bernard Scharfenberger, a priest of the Diocese of Brooklyn and Episcopal Vicar for the area of Queens. Hubbard's final day as Bishop of Albany was April 10, 2014, the day Scharfenberger was consecrated and installed as Bishop of Albany. At the time of his retirement, Hubbard's tenure as bishop was the longest in the Diocese's history at 37 years. Hubbard's post-retirement title is Bishop Emeritus of the Diocese of Albany.