The Rt Revd Justin Welby said it was "a great honour" to welcome Muhammadu Buhari to Lambeth Palace and praised his determination to tackle violence in the West African country.
Reflecting on his first visit in 1978, the Archbishop also said Nigeria offered "more promise and opportunity" than anywhere else he had been to not just in Africa but across "many continents", adding it is "a rare day" when Lambeth Palace does not pray for the country.
In a video streamed live on the Archbishop of Canterbury's official Facebook page, Justin Welby also said: "When Nigerians work together, the world - not just Africa - is affected by that, beneficially.
"So, we pray for the potential and the future of this land, [for Nigeria] to be a place that has a profound effect for good on our world."
The Archbishop was filmed on Tuesday standing next to David Cameron at Buckingham Palace where he referred to Nigeria and Afghanistan as "possibly the two most corrupt countries in the world."
During the conversation at a reception marking the Queen's 90th birthday, the Archbishop interjected to say "but this particular President is actually not corrupt".
A spokesman for Nigeria's president, Muhammadu Buhari described the Prime Minister's comments as "embarrassing" and the Afghan embassy in London branded them "unfair".
David Cameron has been hosting leaders from more than 40 countries for an anti-corruption summit in London this week that he hailed as the "biggest demonstration of the political will to address corruption."