On 9 July 2012, he signed a one-year extension with the club. He secured Wednesday's first win of the season on 21 August with an 89th-minute goal against Birmingham City to see Wednesday win 3–2. He added his second of the season the following Tuesday against Millwall F.C. After being out of favour for most of the season, he returned to the side against Bristol City and scored his 3rd of the season to put Wednesday in front and added his 4th and 5th just fourth days later on 6 April. This was his first league double for Sheffield Wednesday as he secured a crucial win against Blackburn Rovers, equalising against an early Blackburn penalty and scoring the winning goal with a great 25-yard strike in the 78th minute to give Wednesday a 3–2 win. Johnsons 6th of the 2012/13 season came against Yorkshire Rivals Leeds United with a right-footed strike from the centre of the box, headed on from teammate Jérémy Hélan.