Following the transfer of Bishop Patrick Feehan to the Archdiocese of Chicago, Scannell served as apostolic administrator for the diocese from 1880 to 1883.

After a leave of absence for health reasons, he organized St. Joseph's Parish in West Nashville and built its church in 1885.

[1] On 9 August 1887, Scannell was appointed as the first bishop of the newly erected Diocese of Concordia by Pope Leo XIII.

[3] With only 20 resident pastors and a growing Catholic population, Scannell attempted to solve the priest shortage by establishing a preparatory seminary in Belleville, Kansas, laying its cornerstone in June 1890.

During his three-year-long tenure, Scannell also assisted the Sisters of St. Joseph to become permanently established in the diocese, erected fifteen churches, and increased the number of diocesan priests from five to twenty-two.