Heavy security was deployed in central Abuja and the streets were gridlocked as hundreds of APC supporters wearing the party colors of green, white and red entered the venue.
With incumbent President Muhammadu Buhari stepping down after his constitutionally-limited two terms, the frontrunners among the 23 candidates for his post include former Lagos governor Bola Tinubu, Vice President Yemi Osinbajo, former transport minister Rotimi Amaechi and Senate president Ahmad Lawan.
Buhari, who is the leader of the party, has not declared support for any candidate and instructed APC members to "allow the delegates to decide."
"Our objective must be the victory of our party and our choice of candidate must be someone who would give the Nigerian masses a sense of victory and confidence even before the elections," he said last week.
The primaries started on Monday, two days after gunmen killed at least 21 people in an attack on a church in the southwest -- a reminder that security in the elections will be a major issue.
The results of the primary are officially scheduled to be unveiled by 2100 GMT, when the victor is due to make an acceptance speech.
The opposition PDP held its own primary election on May 28 and 29.