He served as a youth leader during his college years and, determining a call to ministry in the Episcopal Church, he went on to complete an M.Div.

[4] In early 2008, Allen stepped down as rector of St. Paul's and became rector of St. Brendan's, telling St. Paul's members that "During the last few years, our (national) Episcopal Church has continued to embrace a wide range of and often conflicting teachings regarding scriptural authority, the divinity of Christ, and affirming other religions at the price of evangelism.

Since I do not agree with their direction, my leadership as a rector would become a divisive issue rather than a reconciling blessing in future parish discussions about how we should participate with and support our diocese and national church.

"[4] As rector of St. Brendan's, Allen became a leader among a group of disparate Anglican realignment congregations in Washington state, including St. Charles in Poulsbo and St. Stephen's in Oak Harbor, both of which had left the Episcopal Church, as well as Reformed Episcopal congregations and unaffiliated Anglican-tradition churches.

[9] In 2016, Allen joined fellow ACNA bishops Eric Menees, Mark Zimmerman, Keith Andrews, and Todd Hunter to streamline the ordination process in western U.S. ACNA dioceses, with a joint exam and a joint examining board that would allow clergy ordained under the standards to serve in any participating diocese.

An episcopal election was held in fall 2023, and Jacob Worley was consecrated and seated as Allen's successor in early 2024.

[13] He also co-led the 2015 meeting in Moscow of ACNA Archbishop Foley Beach and Patriarch Kirill of the Russian Orthodox Church.