While in the Philippines, Bishop Harty administered a large diocese with a Catholic population of 1,368,795. The rigors of his office harmed his health, so he was looking forward to taking over a smaller diocese, such as Omaha, where there were less than 100,000 active Catholics.
After serving the diocese for 11 years from 1916 to 1927, Bishop Harty fell ill with influenza. He was forced to move to Tucson, Arizona, where he was cared for by the Sisters of St. Joseph. He never recovered his health. He died in Arizona in 1927.
During Harty's illness and after his death, Bishop Francis Beckman of Lincoln was appointed apostolic administrator of the Omaha Diocese. He served from 1926 to 1928.
After Bishop Scannell died in 1916, Bishop Jeremiah Harty of Manila was transferred from the Philippines to Omaha.
