In the 2012–13 season, Williams continued to be the first choice goalkeeper and made forty-five appearance for the club this season. But after wasn't included in the starting line-up for the national team, Williams returned to Tranmere Rovers line-up and played in a 3–2 win over Yeovil Town on 13 October 2012. By the end of October, Williams made a good display, where he conceded fourteen goals in fifteen games and kept a clean sheet at least six times. During a period of heavy snowfall in January 2013, an away fixture at Brentford was briefly stopped as Williams was pelted by snowballs thrown from the home supporters. At the end of the 2012–13 season, Williams was offered a new contract by the club. Williams turned down a move to the Championship in favour of signing a two-year contract extension at the club.