Since the 1990s, the Anglican Communion has struggled with controversy regarding homosexuality in the church. In 1998, the 13th Lambeth Conference of Anglican bishops passed a resolution "rejecting homosexual practice as incompatible with Scripture". However, this is not legally binding. "Like all Lambeth Conference resolutions, it is not legally binding on all provinces of the Communion, including the Church of England, though it commends an essential and persuasive view of the attitude of the Communion." "Anglican national churches in Brazil, South Africa, South India, New Zealand and Canada have taken steps toward approving and celebrating same-sex relationships amid strong resistance among other national churches within the 80 million-member global body. The Episcopal Church in the U.S. has allowed same-sex marriage since 2015, and the Scottish Episcopal Church has allowed same-sex marriage since 2017." "Church of England clergy have appeared to signal support for gay marriage after they rejected a bishops' report which said that only a man and woman could marry in church." At General Synod in 2019, the Church of England announced that same-gender couples may remain recognised as married after one spouse experiences a gender transition. In 2023, the Church of England announced that it would authorise "prayers of thanksgiving, dedication and for God's blessing for same-sex couples."

In 2002, the Diocese of New Westminster, in the Anglican Church of Canada, permitted the blessing of same-sex unions. In 2003, two openly gay men in England and the United States became candidates for bishop. In the Church of England, Jeffrey John eventually succumbed to pressure to withdraw his name from consideration to be the Bishop of Reading. In the Episcopal Church in the United States, Gene Robinson was elected and consecrated Bishop of New Hampshire, becoming the first openly gay bishop in the Anglican Communion and in apostolic Christianity. This was highly controversial and led several hundred bishops to boycott the 2008 Lambeth Conference. As an alternative to Lambeth, many of these bishops attended the Global Anglican Futures Conference in Jerusalem.

As of 2004, other Anglican provinces, including the Anglican Church of Southern Africa and the Scottish Episcopal Church, permitted the ordination of gay clergy and others, such as the Episcopal Church in the USA, permitted blessing of same-sex unions as well. The BBC, in 2009, reported that many clergy in the Church of England "already bless same-sex couples on an unofficial basis". In South Africa, the Diocese of Saldanha Bay voted to support blessings for same-sex civil unions. The Anglican Church of Australia's highest court ruled that a diocese may authorise the blessing rites of same-sex unions. In Australia, two dioceses have done so. In 2019, the Southern African Provincial Synod voted to ask dioceses to "reflect and study" a report that recommends allowing each diocese to choose to offer services of prayer for couples in same-sex civil unions.

Many provinces, primarily from the Global South and representing about half of the 80 million active Anglicans worldwide, have responded to these theological disputes by declaring a state of impaired communion with their Western counterparts. Minority groups in Western provinces have stated their opposition to what they consider un-scriptural actions by the churches in England, Canada, Australia, and the United States. Since 2000, some conservative Global South provinces have appointed missionary bishops to the United States and Canada to provide pastoral oversight to disaffected Anglicans. This process, known as Anglican realignment, is considered by the Episcopal Church USA and the Anglican Church of Canada to be an illegitimate incursion into their territories; however, conservative Anglicans argued that the incursions were necessary because of the failure of these churches to uphold orthodox teaching with regard to human sexuality.

As of 2016, "the more liberal provinces that are open to changing Church doctrine on marriage in order to allow same-sex unions include Brazil, Canada, New Zealand, Scotland, South India, South Africa, the US and Wales". In England and Wales, civil partnerships are permitted for clergy. "Neither the Church in Wales nor the Church of England are opposed to clergy being in civil partnerships. The Church of England requests that clergy in civil partnerships vow to remain sexually chaste, but the Church in Wales has no such restriction." The Church of England has allowed priests to enter into same-sex civil partnerships since 2005. In February 2023, the General Synod of Church of England allowed blessings for same-sex couples. As a result, archbishops from 10 conservative provinces of the Anglican Communion declared a state of "impaired communion" with the Church of England and announced that they no longer recognise the Archbishop of Canterbury as "first among equals" among the bishops of the Anglican Communion.