In the years following his self-described "tour of duty" as Presiding Bishop, Allin found a revival of his parish ministry in two seasonal chapels, one in Florida during winter, the other in Maine during summer. In November 1986, Allin began his ministry in Hobe Sound, Florida, having accepted a call to be the fourteenth rector of Christ Memorial Chapel. There he served eight seasons from November through April until 1994. Additionally, Allin served as summer chaplain at St. Ann’s, Kennebunkport, Maine, mid-June through September beginning in 1985 until his last season in 1997. Allin found in both places good work and good communities of people who loved and supported him and Ann. And to his great delight, Allin had the opportunity to play golf year-round.
In early 1986, Allin was elected to the office of Chaplain General of the Community of the Transfiguration, an order of Episcopal nuns in Glendale, Ohio. He served a five-year term with the Sisters, visiting the Mother House three to four times per year and attending to the spiritual and ceremonial needs of the Community. He also traveled to the Dominican Republic, where he visited the Branch House and learned about the Sisters' ministry in a school and medical clinic there. Allin maintained his relationship with the Community beyond his tenure as Chaplain General, visiting and participating in ceremonies and celebrations as he was able.