From 1985 to 1990 Coughlin was pastor at St. Francis Xavier Parish in La Grange, Illinois. He then became Director of the Cardinal Stritch Retreat House in Mundelein, Illinois. In 1995 he began working as Vicar for Priests of the Archdiocese of Chicago under Joseph Bernardin and later Francis George. His work both at the retreat house and in his role as Vicar for Priests—a position that included offering pastoral care to priests, including those involved in sexual abuse cases—would later lead to accusations of impropriety (that he was somehow involved with the overall problem of covering up sex crimes within the Catholic Church) later in his career.