The consecration in 2003 of an openly homosexual priest as a bishop by the Episcopal Church and the blessing of gay unions by the U.S. and Canadian churches led to tensions within the communion, especially with more conservative African churches, some of which broke their ties the Episcopal Church; the 1998 Lambeth Conference had rejected homosexual practice as incompatible with the Bible and refused to advise blessing same-sex unions and ordaining individuals involved in such unions. In 2005 the two North American churches were asked to withdraw from the Anglican Consultative Council, which they did voluntarily, attending as observers in June, 2005. In September, however, the Anglican Church of Nigeria removed explicit references to being in communion with the Church of England from its constitution, again raising the possibility of a schism in the Anglican Communion.

Following the Episcopal Church's call in 2006 for a moratorium on the consecration of openly homosexual bishops, a move that many Anglican conservatives regarded as inadequate, the archbishop of Canterbury proposed that Anglicans adopt a formal covenant concerning their shared beliefs, a suggestion that seemed likely to exclude the Episcopalians from full membership in the Anglican Communion or split the American church. Homosexuality is not the only issue dividing the communion, however; the ordination of women as priests and bishops is also a subject on which the churches are split. A 2007 proposal by the Anglican primates to establish a separate vicar for conservative American parishes was strongly opposed by Episcopal bishops, who regarded it as foreign interference in their provincial affairs and contrary to the principles of the Episcopal Church and the nature of the Anglican Communion.

Nigerian primate Peter Akinola subsequently installed a Virginia bishop as leader of a conservative North American Anglican group, despite a request not to do so from the archbishop of Canterbury. In 2008 conservative Anglicans met in Jerusalem and formed their own organization, but did not break completely with the Anglican Communion. Many conservatives, however, did not attend the subsequent Lambeth Conference (July, 2008). The Episcopal Church ended its moratorium on consecrating openly homosexual bishops in 2009.