Onyeka, 28, initially joined on loan in January and made 14 appearances for Frank Lampard's side during the second half of the season as Coventry won the Championship. His deal contained a clause ensuring a permanent transfer in the event of promotion, which has now been activated.
The midfielder was direct about his motivations and ambitions for the campaign ahead.
"I'm really excited for the new season with Coventry," Onyeka told club media. "When I first joined last season, I came here with two goals: to win the Championship and help Coventry get promoted to the Premier League.
"I'm really happy to now be a Coventry player back in the Premier League. I will give everything to the team, fight for every ball, fight for my team-mates and bring my experience. My ambition now is to help the team stay in the Premier League and finish as high as we can."
For Coventry, completing the signing removes any uncertainty over a player who was an important contributor to their promotion campaign, while giving Lampard a committed, experienced central midfield option as the club prepares to compete in the top flight.
Onyeka's combative style and experience in the Premier League from his time at Brentford make him a practical addition for a newly promoted side that will face a significant step up in quality next season.
Whether Onyeka can make the step up from Championship to Premier League football as a consistent starter will be the test that defines his contribution at Coventry over the coming season.
It will be a fascinating new campaign for both player and club.