From 1984 to 1990, McDonnell was pastor of Holy Trinity Parish in Manhattan. He briefly served as Episcopal Vicar of West Manhattan (1989–1990). In 1990, he became Chief Operating Officer of the archdiocesan Catholic Charities, as well as being assigned to help run Covenant House following the resignation of Rev. Bruce Ritter. McDonnell then served as pastor of St. John and St. Mary Parish in Chappaqua from 1993 to 2002, during which time he oversaw a major renovation construction project to accommodate the growing Catholic community.