Following the loss, Scobbie said the defeat left him "heartbroken". Ahead of the 2009–10 season, Scobbie was among three players to be linked a move away from Falkirk, as he was keen to sit down with the club's board to discuss the fresh terms. Scobbie made his European debut for the club against FC Vaduz of Liechtenstein, but lost 2–1 in a two-legged tie. The season started without the manager, John Hughes, who left for Hibernian. In October, Scobbie sustained a recurrence of his pelvic problems, which caused him to be pulled out of Scotland's Under-21 squad. Scobbie revealed he had taken 12 injections and unsuccessfully had a hernia operations twice. In late January, Scobbie recovered from injuries. Following his return, Scobbie was unable to help the club survive relegation and was relegated to Division One. The 2010–11 season was proved to be unsuccessful for Scobbie, as he made thirty-six appearances in all competitions and scored once against Dunfermline Athletic on 15 February 2011, in a 1–1 draw. After the season, Scobbie was linked with SPL clubs Kilmarnock and St Mirren. On 1 April 2012, Scobbie played as Falkirk beat Hamilton Academical 1–0 to win the Challenge Cup. In May 2012, Scobbie announced he is to leave the club this summer and says his departure was ""inevitable"". In his last appearance against Ayr United on the last game of the season, Scobbie was given the captaincy and scored the opening goal from the penalty, as Falkirk won 3–2. Scobbie left Falkirk under freedom of contract in May 2012 and signed a two-year contract with St Johnstone. Scobbie made his debut for the club, where he made his first start, in a 2–1 loss against Aberdeen on 18 August 2012. However, Scobbie was unable to regain his first team place at St Johnstone, as he spent on the bench and had his own injury concerns. At the beginning of the 2013–14 season, Scobbie played four Europa League matches, including the 1–0 win against Norwegian side Rosenberg in the second round of the Europa League first leg. St Johnstone would later be eliminated by Minsk in the drawing 1–1 in the second leg of Europa League after it went on penalties. In the league, Scobbie would be often used in first team ins and out in his second season at the club.