The service, which also marked the Prince's 59th birthday, acknowledged the work done by Jesus House in the local community as well as the growing contribution made by Pentecostal and black majority churches in the UK.
Other attendants of the service were the Mayor of Barnet, the leader of the local council, local MPs and the Bishop of London, the Rt Rev Richard Chartres.
Prince Charles began by thanking Jesus House for the welcome he received, "I can't tell you what a joy it is to worship with you today. All I can tell you is that there is nowhere I would rather be on my birthday. You have given us both such a wonderful, warm and happy welcome and all I can tell you is that we shall leave here with our spirits well and truly raised."
During his speech, the Prince of Wales praised the work of Jesus House and of the black majority churches in the UK.
"You are all a marvellous example of how so many people whose families originate from the Commonwealth, have yourselves brought new life into the Christian church in the United Kingdom thereby completing the cycle started by missionaries from Britain so many years ago. So we have that to thank you for," he said.
Prince Charles said he was "so impressed" by Jesus House's active involvement in the local community. Members of the congregation run yearly free car wash events and the Spreading Christmas Cheer programme, where they work in London Underground stations giving away hot drinks and mince pies. They also visit the elderly and drop-in centres.
"I must also say that a huge positive contribution to British society is made by a great number of church-going black people," he continued. "I want you to remember that it is highly appreciated by me and more and more by other people. Too often, it seems that the media are interested in the negative and stereotypical but you, if I may say so, are a wonderful and shining example."
The Prince also spoke of his desire to develop link and collaboration between his Prince's Trust and the black churches, something he had discussed earlier in the day in a meeting with pastors and bishops.
The Prince of Wales concluded, "I wish I had known about this church long ago. I pray, ladies and gentlemen, that you continue in your wonderful work for the spirit and that you are inspired by our Lord for many years to come."
Pastor Agu Irukwu, the Senior Pastor of Jesus House said it had been a "special day" and an "honour" to be visited by the Prince of Wales and Duchess of Cornwall.
Jesus House Youth Pastor, Bajo Akisanya, told Christian Today that the visit had been "momentous".
"He acknowledged some very unseen work and I think that's one of the most wonderful things," he said.
Jesus House was founded in 1994 and is a parish of the Redeemed Christian Church of God.