About 1833 or 1834, when Allen was captain of the Ann, the crew rose in mutiny and killed one of the mates.
He bought 809 ha (2000 acres) of land in the neighbourhood of Port Gawler with his friend Captain John Ellis.
He took an interest in the Church of England and in the words of Bishop Augustus Short became "the greatest temporal benefactor - next after the Baroness Burdett-Coutts - whom the diocese has yet been permitted to know".
On 24 May 1849, when the foundation-stone of St Peter's College was laid, William Allen and the Society for Promoting Christian Knowledge were referred to as "the Principal Founders".
Allen visited England again in 1853, upon his return to South Australia he retired from his pastoral activities.