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From 1905 to 1909, McGuire served as Archdeacon for Colored Work in the Diocese of Arkansas , becoming the church's highest ranking African American and the first to achieve the rank of Archdeacon, where he zealously labored to increase the number of missions from one to nine. He also encountered opposition from the local Episcopal bishop who believed blacks should be separated from whites and placed in their own church jurisdiction. Eventually McGuire resigned and moved to Cambridge Massachusetts where he established St. Bartholomew’s Church for West Indians living in the Boston area. While in Cambridge, McGuire studied at Boston College of Physicians and Surgeons, receiving his M.D. degree in 1910. When his small church was not recognized by the Episcopalian diocese, McGuire resigned in 1911. As he traveled across the U.S. he became even more discouraged by the dismal prospects of blacks in the Episcopal Church and left the denomination.

In 1913 McGuire returned to the West Indies, settling in British-controlled Antigua to care for his sick mother. While there he volunteered at a local perish , serving as a minister in the Church of England, and gained acclaim for practicing medicine on the island. When a strike of local sugar cane workers led to rioting and burning of the sugar cane fields, British colonial officials urged local and religious leaders to oppose the strikes but McGuire refused and urged them to provide the workers with decent, living wages.