Clyne's contract will now run until summer 2026, whilst Matthews has penned a new two-year deal.
The defender and goalkeeper have spent nine and four seasons respectively with the Eagles’ senior squad.
In that time, Clyne has made 238 appearances for the club – including 19 in all competitions this season – whilst Matthews has provided valuable competition in the goalkeeping department, making his Palace debut against Liverpool in 2023/24.
Chairman Steve Parish said: “We are pleased to be retaining Nathaniel and Remi’s services next season.
“They are two highly dependable members of the squad who set a high standard in their hard work, leadership and professionalism, and they will continue to play an important role at the club.”