In the 2012–13 season, Daly started his season, playing in both legs of the third round qualifier of the Europa League against Russian side Dynamo Moscow. In the first leg, Daly provided an assist for Keith Watson in a 2–2 draw. However, in the second leg, the club would lose heavily in a 5–0 loss. Daly scored his first goal of the season, on the opening game of the league campaign, in a 3–0 win over Hibernian. In a 3–3 draw against Kilmarnock, on 16 November 2012, Daly scored a brace. In a 4–4 draw against Inverness, on 15 December 2012, Daly assisted Josh Meekings before scoring another brace for himself. Throughout the Scottish Cup campaign, Daly scored a brace in a fourth round tie against Stranraer; followed up by a double assist for Russell before setting a goal for himself, in a fifth round win over Rangers and in the semi-final, Daly scored twice, in a 4–3 loss against Celtic. Later in the season, Daly would score nine more goals in the league and finish second top-scorer behind Johnny Russell.