Bootkoski served as bishop of the Latin Church Diocese of Metuchen in New Jersey from 2002 until March 8, 2016; he was replaced by Monsignor James Checchio.

In 1983, He became pastor of St. Mary of the Assumption Parish in Elizabeth, New Jersey and was named by the Vatican as an honorary prelate with the title of monsignor in 1991.

[1][2] On January 31, 2003, Bootkoski approved an $800,000 settlement to ten people who had alleged sexual abuse when they were minors by five diocesan priests.

[5] According to Cardinal Donald Wuerl, nobody from the Diocese of Metuchen informed him of these settlements, even after the retired McCarrick began living on the grounds of a seminary in the Archdiocese of Washington.

[5] Having passed the normal retirement age of 75, Bootkoski's resignation as bishop of the Diocese of Metuchen was accepted by Pope Francis on March 8, 2016.