The 2012–13 season saw MacDonald play in both legs of Hearts Europa League play-off round matches against Liverpool, including playing in the first leg just 24 hours after becoming a father for the first time. However, Hearts were eliminated from the Europa League after losing 2–1 on aggregate. In a 1–0 loss against Celtic on 7 October 2012, MacDonald was stretchered off after colliding with Charlie Mulgrew. After the match, Manager John McGlynn said he was fine by half-time and was making a recovery despite having been unconscious. MacDonald helped the club reach the Scottish League Cup final after beating Inverness CT in the semi-final, winning 5–4 in a penalty shootout following a 1–1 draw. Hearts went on to lose to St Mirren 3–2 in the final. MacDonald was ever present at the club in the 2012–13 season.