The pontiff was presented at All Saints Anglican Church with gifts from the Anglican Church, including homemade jams and mustards, and a Simnel cake - a traditional English treat eaten on the fourth Sunday of Lent.
Speaking on Premier News Hour, Warden at All Saints, Philippa Hitchen, said the visit had great historical significance.
"We saw St John Paul II coming to Canterbury Cathedral many years ago and we say Pope Benedict visit Westminster Abbey in 2010 but this the first time a pope has visited an Anglican church in his own diocese and the first time he's visited a regular parish church," she explained.
She also told Premier's News Hour what the pope had to say.
"He said that his visit here to All Saint's Church was another symbol of the important steps we're making together for Christian unity."
Answering questions from members of the church, the pope revealed discussions were underway for a joint visit to South Sudan with the Archbishop of Canterbury Most Reverend Justin Welby.
He presided over an evensong service with the bishop of the Anglican Diocese in Europe Most Rev Robert Innes and blessed a newly commissioned icon of Christ the Saviour.
Marking its 200th years, All Saints parish - and its twin Catholic parish in Rome - pledged to offer a meal ever Friday evening for the poor near the Ostiense railway station in Pope Francis' name.
The Anglican community also said a quarter of the 200 English bibles printed to commemorate the parish's milestone would be donated to prostitutes in Western Africa.
The bibles will be distributed by a network of sisters who help victims of human trafficking, many of whom end up in forced prostitution.
Listen to Aaron James speaking to Philippa Hitchen here: