During his final year of studies, Bishop Modeste Demers was touring Europe to recruit priests for the Diocese of Vancouver Island and Lootens offered his services.

[6] After five years of missionary work at mining camps and Native American villages in the Cariboo and Fraser Valley region, Lootens was accepted into the Archdiocese of San Francisco in June 1857.

[7] On March 3, 1868, Lootens was appointed the first Vicar Apostolic of the Idaho Territory and titular bishop of Castabala by Pope Pius IX.

[5] He received his episcopal consecration on the following August 9 from Archbishop Joseph Sadoc Alemany, with Bishops Thaddeus Amat y Brusi and Eugene O'Connell serving as co-consecrators, at Old St. Mary's Cathedral in San Francisco.

[6] In March 1873, Lootens wrote: "The Catholic population of the Vicariate Apostolic of Idaho having dwindled away to such an extent that the remainder does no longer afford us...the bare necessaries of life.

Lootens returned to British Columbia, where he began his priestly ministry, and was named an auxiliary bishop of the Diocese of Vancouver Island.