In early 1986, he was named temporary assistant pastor at St. Regis Church in Birmingham and adjunct professor of moral theology at SS. Cyril and Methodius Seminary in Orchard Lake. He was made pastor of St. Patrick's Parish in Union Lake in July that year. In 1987, Nienstedt was appointed to reorganize his "alma mater" Sacred Heart Seminary. He became its Rector in 1988. He became an Honorary Prelate of His Holiness in 1990 and pastor of the National Shrine of the Little Flower in Royal Oak in 1994.