In January 2011, Walters scored twice for City in a 2–0 FA Cup third round replay win at Cardiff City. It took him until the end of March 2011 to find the back of the net in the Premier League again, scoring in a 4–0 win over Newcastle United. He scored in the next match against Chelsea and was named as Man of the Match. Following the match, Tony Pulis spoke of his delight at Walters' improved performances. "Jon's come from the Championship and sometimes it takes time to have the confidence and the belief to make the step up. He had an up-and-down start but he's been fantastic for us. He's certainly my type of player, he gives everything, he never stops and whatever you've paid him, you know he's earned it."
Walters scored twice in Stoke's 5–0 rout over former club Bolton Wanderers in the FA Cup semi-final at Wembley to help Stoke into their first FA Cup Final. Walters described it as the pinnacle of his career. Walters ended the 2010–11 season as joint top goalscorer with Kenwyne Jones, both having scored 12 goals. His first goal against Bolton in the semi-final won Goal of the Season. He played in the 2011 FA Cup Final against Manchester City as Stoke lost 1–0.
Walters played in his first European match on 28 July against Hajduk Split where he scored the only goal in a 1–0 Stoke win. He signed a 12-month contract extension in August 2011. Walters went on to play in 31 matches during the first half of the 2011–12 season scoring seven goals. In March 2012, Walters won the Sir Stanley Matthews Potteries Footballers of the Year award for 2012. Speaking after picking up the award, Walters revealed that he would like to remain at Stoke for the rest of his career. By 21 April 2012, Walters had played in 50 matches during the 2011–12 campaign and scored nine goals of which five were penalties. This led to Walters being criticised by some Stoke supporters but he was backed by his manager. On his 100th appearance for Stoke, Walters scored twice against his old club Bolton Wanderers in a 2–2 draw, a result which relegated the "Trotters".