After Southampton had won promotion to the Premier League there was speculation linking them with a £7m for Hooper at the start of the 2012–13 season. However, Hooper stated that he was happy at Celtic and was looking forward to playing Champions League football. On 1 August 2012, Hooper started the season in scoring form, in Celtic's 2–1 victory against HJK Helsinki in the first leg of the Champions League Third Qualifying Round. On 25 September 2012, Hooper scored all 4 goals in Celtic's Scottish League Cup tie against Raith Rovers at Celtic Park, the match finished 4–1. On 29 September 2012, Hooper scored the first goal in a 2–0 victory over Motherwell at Fir Park, this resulted in Celtic going to first spot in the Scottish Premier League. Hooper scored his seventh goal in four matches, against Spartak Moscow in the UEFA Champions League; Celtic won the match 3–2 at Spartak Stadium, recording their first ever away victory in the UEFA Champions League proper. During January 2013, Hooper scored braces against Hearts and Dundee United in high scoring wins at home for Celtic, and also scored the only goal in a 1–0 away win at Motherwell. That run of goalscoring saw him win the SPL Player of the Month Award. Celtic clinched their second successive Scottish Premier League title on 21 April 2013 with a 4–1 win over Inverness Caledonian Thistle at Parkhead. Hooper scored twice in the match. On 26 May 2013, Hooper scored twice for Celtic in their 3–0 win over Hibernian in the Scottish Cup Final.