In May 2018, despite their relegation to League Two, Bury offered Lowe the position of full-time manager on a two-year contract to the end of the 2019–20 season.

[5] He spent a year at Chester, which included scoring twice in a shock FA Cup 3–0 win over Nottingham Forest on 3 December 2005[6] before leaving the club by mutual consent shortly after the return of manager Mark Wright.

[8] His transfer was not made permanent and he was not included in the side which clinched promotion in the play-off final against Rochdale at Wembley Stadium.

On 2 July 2008, Lowe returned to Chester on a two-year deal, becoming the club's fifth summer signing after Anthony Barry, Jay Harris, David Mannix and Paul Taylor.

[9] Lowe scored twice including a penalty, in his first home game back for Chester against Leeds United in a 5–2 loss in the League Cup on 12 August 2008 and repeated the feat in a 5–1 thrashing of Barnet later in the month.

On 1 March 2011, Lowe broke a 53-year-old club record by scoring in eight consecutive league games in a 3–0 victory over Shrewsbury Town at the Greenhous Meadow.

[18] On 23 November 2015 Lowe rejoined his former club Crewe Alexandra on loan until 5 January 2016,[19] and in his first appearance scored a stoppage time winner at Colchester United.

[24] Following the sacking of manager Lee Clark in October 2017, Lowe was appointed caretaker-manager, taking charge for Bury's FA Cup first-round tie at National League side Woking.

[25] He remained in charge for six games (two wins, two draws, two defeats) until 22 November when Chris Lucketti was appointed Clark's successor, with Lowe becoming player-coach again.

[3] After a shaky start to the season in which the new team found its feet, Bury had reached fourth place in the table when they travelled to promotion rivals Mansfield Town on Boxing Day.

In addition, Lowe led them to the semi-final stage of the EFL Trophy, Bury's best-ever showing in this tournament, before they were defeated by League One Portsmouth.

[30][31][32] On 5 June 2019, Lowe was announced as manager of Plymouth Argyle,[33] guiding them to a third-place finish and an immediate return to League One in a season interrupted by the COVID-19 pandemic in the United Kingdom.

[41] Lowe explained in an interview with The Guardian that he wanted to instil a "winning philosophy" and that, by outscoring their opponents, Bury would have a greater chance of achieving that goal.