In 2003, he returned to the Scottish Executive as Deputy Minister for Finance and Public Services. During his time there his department piloted the Local Governance (Scotland) Act, which changed the elections for local authorities in Scotland to a proportional representation system. Following Nicol Stephen's election as party leader and succession as Deputy First Minister of Scotland in 2005, Scott was appointed to the Cabinet as Minister for Transport. He was re-elected with an increased majority in May 2007, and held the largest margin by percentage, 50.1%, of any MSP over their closest challenger.