Thomas, 25, joined the club from Burnley back in 2023 and has since gone on to play 129 games, scoring 10 goals.
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The defender played a key role for Frank Lampard as they earned promotion to the Premier League, scoring the goal that sealed the deal against Blackburn.
Coventry have now confirmed that Thomas has signed a new contract with the club, although the length remains undisclosed.
He told the club's official website: "I’ve really enjoyed my time here and it has been amazing to be a part of such a historic achievement in helping the club get back to the Premier League.
“Those memories will live with me, my friends and my family forever and I’m excited for what’s ahead!"