Upon leaving Totton, he joined the Archbishops' Council staff team as National Mission and Evangelism Adviser until his ordination to the episcopacy.

Bayes is the Visitor of St Peter's College, Oxford;[12] he was chosen from among the Church's diocesan bishops, and may serve until he ceases to be one.

[16] In June 2016 Bayes "called for far-reaching change in the church's attitudes to lesbian and gay people and a meaningful welcome to Christians in same-sex relationships".

[17] He supports dropping the requirement for gay Christians to be celibate, saying "I've learned to respect the experiences of people who want to celebrate and express their sexuality, and be within the church".

[17] He contributed a chapter to the book Journeys in Grace and Truth: Revisiting Scripture and Sexuality (2016), which aims to show how it is "possible to hold a positive view of same-sex relationships while being a biblically rooted evangelical".

[the political culture was] adversarial, scratchy, exhausted (...) You see clear illiberalism in eastern Europe, you see the rise of the extreme right in France, and you see what you see in the United States … Basic decencies have been lost.”[22] In the Diocese of Liverpool, Bayes has sought to galvanise all members of the churches, younger and older, around a vision named "Bigger Church, Bigger Difference", with the stated theme "Making a Bigger Difference — More people knowing Jesus, more justice in the world"[23] This has been further embedded through the call to a Rule of Life[24] within the diocese.