The church had a close relationship with a number of almshouses in the area, particularly the Fishmonger’s Company Almshouse and the Draper’s Company Almshouse. The Fishmonger’s Company, paid 40 marks in 1607 for the privilege of using a large pew in the church to seat their alms people who came from their alms house of St. Peter’s. The 1629 rebuilding project caused hostilities with the Fishmongers Company, as they demanded the continuation of their right to use the same pew in the same location in the church. This would have been a logistical impossibility after the rebuilding, as the original location of the pew was now be in the middle of the churchyard.
A number of chapels also existed in the church and parish, as evidenced in the 1725 visitation. The lecturer of the church, Francis Phillips, served the King’s Bench chapel, which was maintained by fees from the prison. There was also two chapels associated with local almshouses, the Fishmonger’s almshouse and the Drapers’ almshouse. Both these chapels were served by almsmen. Within the Marshallsea prison, there was a chapel served by a Mr. Gainham in 1725 and maintained by collections from the prisoners. By 1840, there were six Anglican chapels in the parish; St. John’s Chapel and the Philanthropic Chapel on Borough Road, the Magdalen Chapel on Blackfriars Road, the chapel at the Marshalsea Prison, the chapel at the Queen’s Bench Prison and a chapel at the parish school.