On June 18, 1864, Colonel B.G. Farrar, commander at Natchez, and former schoolmate of Elder's at Mt. St. Mary's, issued an order requiring the clergy to include prayers for the President of the United States in their services, as a ""public recognition of allegiance under which they live, and to which they are indebted for protection..."" Elder responded with a lengthy letter of protest in which he explained that his declining to submit had no political significance, but the "Liberty of the Church to discharge her divine functions, without interference form other persons." Brigadier General James Madison Tuttle issued an order for inforcement, which was stayed at Elder's request, pending input from the War Department. Elder wrote to President Abraham Lincoln explaining that his refusal was based on the authority of the church to regulate church services. Senator Francis Kernan responded, saying he had met with Secretary of War Edwin M. Stanton and Stanton indicated that he would communicate to Tuttle to remedy the situation so there would be no further interference. Elder subsequently wrote thanking Stanton for the protection extended to religious freedom, and asking that the ruling be made known to other commanders. Later, Colonel Farrar was placed in command of Natchez; he noted Tuttle's order had neither been rescinded nor was being obeyed. General Mason Brayman, the next commander, took a harder stance, saying "...military orders are to be followed, not discussed..." and issued an order for Elder to be sent to jail in Vidalia, Louisiana. Federal troops took Elder to Vidalia for a few weeks. After Washington officials intervened, Brayman ordered the release of Elder on 12 August 1864. During his time in Natchez, a yellow fever epidemic broke out in 1878. Ministering to the sick, Elder caught the disease. He survived but lost six diocesan priests. At the time he arrived in Natchez the diocese had eleven missions (churches), nine priests and 10,000 Catholics. When he left, there were forty-one churches, 25 priests, six religious houses for men, five convents, thirteen parish schools and 12,500 Catholics. On January 30, 1880, he was transferred to Cincinnati, becoming coadjutor bishop with the right of succession to Archbishop Purcell, whom he succeeded July 4, 1883. Archbishop Elder was third bishop and second archbishop of Cincinnati. He became bishop at a time of great financial difficulty in the archdiocese.