Keshi died on June 8 in Benin at the age of 54, months after the end of his four-year spell as coach of the Super Eagles.
He was one of the only two people to have won the African Cup of Nations both as player and as coach in 1994 and 2013.
The remains of the former captain of the senior national team were brought through the centre aisle of the church with his children, family members and friends following behind.
Present at the ceremony is a delegation of Nigeria Football Federation, led by its President, Amaju Pinick.
Also present is the Chairman of the Edo State Football Association, Frank Ilaboya, and former team mates of the late football strategist, including Austin Eguavoen.