Betemit's agreement is worth $1 million. Pena's contract is for $660,000.
The Royals also announced Thursday that they did not tender a contract to infielder Josh Fields, making him a free agent. Fields missed most of last season after undergoing surgery on his right hip.
The 29-year-old Betemit batted .297 with 13 homers and 43 RBI in 84 games after he was promoted from Triple-A Omaha on May 25.
The 28-year-old Pena hit .253 in 60 games while serving as Kansas City's backup catcher in 2010.