At the end of the 2015–16 season, Bolton confirmed that he would be leaving when his contract expired at the end of June.[6] On 24 July 2016 it was confirmed that he had joined Bolton's close neighbours Bury on a twelve-month contract.[7] He scored his first goal for Bury against Burton Albion in an EFL Cup tie on 10 August 2016.[8]
On 8 March 2018, Maher signed for National League side FC Halifax Town on a deal until the end of the 2017–18 season.[11] On 18 August 2018, Maher extended his stay by agreeing a new two-year deal.[12]
Halifax announced on 17 August 2020 that Maher extended his deal for a further two years.[13]
Ahead of the 2021–22 season Maher was installed as the new club captain, replacing the departing Nathan Clarke.[14] After advancing to the play-offs following a 4th place finish, Halifax were defeated by Chesterfield in the eliminator round, thus ending their bid to reach the Football League.[15] Maher was voted into the National League Team of the Season.[16]
On 6 June 2022, Maher announced he would be leaving Halifax following the conclusion of the 2021–22 season, he stated upon his departure "To be your captain over the last 18 months has been a massive honour. To the players - it's been one hell of a season with a great dressing room to manage and there is no doubt that you all deserve to be achieving the best in your careers whatever they may be."[17]
Grimsby Town
On 15 June 2022, following their promotion to the Football League, Maher signed for Grimsby Town ahead of the 2022–23 season,[18] reportedly rejecting an offer from Oldham Athletic who were hopeful of signing him.[19]
Maher was part of the Grimsby team that reached the FA Cup quarter final for the first time since 1939, he played the full 90 minutes of the 2–1 win away at Premier League side Southampton that secured that achievement.[20][21]