In April 2018, Miller and teammate Lee Wallace were suspended by the club pending an internal investigation into an altercation with manager Murty, in the aftermath of the 2017–18 Scottish Cup semi-final which Rangers had lost 4–0 to Celtic. Miller was fined by Rangers and left the club at the end of his contract. Five months after the incident for which they were disciplined, Miller and Lee Wallace won an appeal at a SPFL tribunal against the action taken against them, with the expectation they would make a financial claim against Rangers for the fines imposed. Over his three spells at the club, he made 301 appearances in all competitions, scoring 116 goals.
Miller was appointed player-manager of Scottish Premiership club Livingston in June 2018. He scored his first goal for the club on his third appearance, netting the only goal of a 1–0 victory over Dumbarton on 21 July in the group stage of the 2018–19 Scottish League Cup. He left the role on 19 August, with his departure being an 'amicable agreement' following discussions between Miller and the club hierarchy; they would have preferred him to give up playing and focus solely on the managerial role, which he was not prepared to do at that time. Livingston said that they had asked Miller to focus on his tasks as manager, but Miller had been unwilling to end his playing career. The following week, Miller's former Scotland teammate Gary Holt was appointed his successor at Livingston.
Miller signed a two-year playing contract with Dundee on 29 August 2018. He failed to score in his first seven matches for the club but then scored five in three games, including a hat-trick at home to relegation rivals Hamilton Academical on 5 December. Dundee finished in bottom position in the Premiership table and were relegated to the Scottish Championship, with Miller leaving the club 'by mutual consent' during the summer off-season.