Bethea became an unrestricted free agent in 2014 and drew interest from multiple teams, including the Detroit Lions, San Francisco 49ers, Philadelphia Eagles, Green Bay Packers, and Kansas City Chiefs.
On March 12, 2014, the San Francisco 49ers signed Bethea to a four-year, $21 million contract with $15.02 million guaranteed and a signing bonus of $5.25 million.
Head coach Jim Harbaugh named Bethea the starting strong safety to start the season, alongside free safety Eric Reid. He started in the San Francisco 49ers' season-opener at the Dallas Cowboys and recorded six solo tackles and a pass deflection in their 28–17 victory. In Week 10, Bethea collected a season-high eight combined tackles, broke up a pass, and intercepted a pass by Drew Brees during a 27–24 overtime victory at the New Orleans Saints. On December 20, 2014, Bethea recorded a season-high tying eight combined tackles, two pass deflections, and returned an interception by Philip Rivers for a 49-yard touchdown during a 38–35 overtime loss to the San Diego Chargers in Week 16. His touchdown occurred in the second quarter and marked the first score of his career. On December 24, 2014, it was announced that Bethea was selected to be an alternate for the 2015 Pro Bowl. On December 28, 2014, it was announced that the San Francisco 49ers and head coach Jim Harbaugh decided to mutually part ways after the 2014 season. He finished his first season in San Francisco with 86 combined tackles (72 solo), ten pass deflections, four interceptions, a forced fumble, and a touchdown in 16 games and 16 starts.