Miller resumed his interrupted studies at the
Allegheny Theological Seminary in the fall of 1865 and completed them in the spring of 1867. That summer he accepted a call from the
First United Presbyterian Church of
New Wilmington, Pennsylvania. He was ordained and installed on 11 September 1867. Miller held firmly to the great body of truth professed by the
United Presbyterian Church, in which he had been reared, but he did not like the rule requiring the exclusive singing of the
Psalms, and he felt that it was not honest for him to profess this as one of the articles of his Christian belief. He therefore resigned from his pastorate to seek membership in the
Presbyterian Church (USA). In his two years as pastor, nearly two hundred names were added to the church roll. The Old and New School Presbyterian Churches were reunited as the Presbyterian Church (USA) on 12 November 1869, and Miller became pastor of the
Bethany Presbyterian Church of
Philadelphia just nine days later. When he became pastor at Bethany the membership was seventy five and when he resigned in 1878 Bethany was the largest Presbyterian church in Philadelphia, having about twelve hundred members. Miller then accepted the pastorate of the New Broadway Presbyterian Church of
Rock Island, Illinois. In 1880, Westminster College, his
Alma mater conferred on him the degree of
Doctor of Divinity and later in the same year came the invitation to undertake editorial work for the
Presbyterian Board of Publication in Philadelphia. Hence, Miller had to resign the Rock Island, Illinois pastorate. In Philadelphia, Miller became interested in the
Hollond Mission and eventually became its pastor. During the sixteen months of the pastorate the church membership grew from 259 to 1,164 and Sunday School membership climbed from 1,024 to 1,475. On 29 October 1899,
St. Paul Church in West Philadelphia was organized with sixty-six members. Miller was chosen temporary supply and became pastor in 1906. Miller remained pastor until the year of his death, 1912. The church at that time had 1,397 members. ==Family==