After Walkowiak returned to Cleveland in 1988, Bishop Anthony Michael Pilla appointed him as vice-chancellor and as a professor of canon law at Saint Mary Seminary. In 2006, Walkowiak was also appointed as pastor of Saint Joan of Arc Parish in Chagrin Falls, Ohio.[1] He also served as a member of the council of priests and as an associate judge of the court of appeals.[1]
Walkowiak released a statement on November 27, 2019, in which he supported the decision of Reverend Scott Nolan, pastor of St. Stephen Parish in East Grand Rapids, Michigan, to withhold the Eucharist from Sara Smolenski. A town judge, Smolenski told the local media that Nolan notified her before mass that she could not receive communion because of her same-sex marriage. She also said that Nolan had given her communion the week before.[4][5]
On May 27, 2021, Walkowiak announced that Pope Francis had laicized Reverend William Langlois. The diocese had received allegations in 2018 that Langlois had sexually abused a parishioner when they were a minor between 1999 and 2006. The diocese immediately suspended Langlois, notified local authorities, and started an internal investigation.[6]