Although tipped as favorites for the title and promotion before the season had even begun, the club struggled to immediately adapt to life in the new division, ultimately costing manager Mick Harford his job.

Richard Money was appointed as the new manager soon after, eventually leading the club to an unbeaten run of 14 games towards the end of the season that propelled them to a second-place finish in the league.

[25] On 11 August, with the news that left-back Lewis Emanuel was to be sidelined for three months with a broken toe sustained in the game at Kingsmeadow, Luton signed Grays Athletic defender Fred Murray on a six-month loan deal.

[26] Murray started in the team on the same day in Luton's first home game of the season – a 4–1 victory over Mansfield Town that saw centre-back George Pilkington score his first two goals for the club.

[30] Long-term injuries to forwards Ryan Charles and Liam Hatch left Luton short on attacking options, resulting in striker George Donnelly signing on a one-month loan from Plymouth Argyle on 28 August.

[38] Peterborough United striker Ben Wright signed on a one-month loan on 29 September, boosting Luton's attacking options in the wake of further injuries and suspensions.

Luton were 13 points from the top of the table and, in a club statement, managing director Gary Sweet admitted that results and performances were not up to the standards expected at the beginning of the season.

[40] Neilson continued on an unbeaten run of five matches, including an FA Cup victory over Grays Athletic, until Luton appointed former Walsall boss Richard Money as permanent manager on 30 October.

[46] A 2–2 home draw with Cambridge United the next week saw Luton let in two late goals; a game that could have ended in a loss had Kevin Pilkington not saved a penalty.

[49] Midfielder Andy Burgess, who was signed only in May 2009 and had made 10 appearances for the club, joined promotion rivals Mansfield Town on an initial one-month loan with a permanent transfer arranged for January 2010.

[50] In a busy day of transfer dealing, striker Steve Basham, sparsely used since his arrival in the summer, completed a two-month loan to Hayes & Yeading United.

[51] Luton signed Kidderminster Harriers' top scorer Matthew Barnes-Homer on a two-and-a-half-year contract for a five-figure fee, with the permanent transfer taking place in January 2010.

[53] A 1–0 home defeat to Kettering Town on 2 December, followed by a 0–0 draw to Chester City three days later, resulted in Luton finding themselves in seventh place in the table and four points off of a play-off position, albeit with two games in hand over some teams.

[61] On 5 January, with the transfer window now open, Luton signed young St Albans City players Jonathan O'Donnell and Godfrey Poku on 18-month contracts.

[62] O'Donnell had previously spent time in the youth set-up at Luton's local rivals Watford and Milton Keynes Dons, while Poku was highly rated by St Albans manager Steve Castle.

[80] Luton's ten-game unbeaten away record in the league continued with a 0–0 draw at their promotion rivals York City on 16 February, pushing the club up to fourth place in the table.

[81] The club's poor league form at Kenilworth Road, in which only three games out of ten had ended in Luton winning, continued with a fifth home defeat – a 2–1 loss to AFC Wimbledon.

[84][85] A last minute winner from Tom Craddock in a 2–1 victory over Forest Green Rovers on 9 March propelled Luton to third place in the table, the club's highest position since early September.

Kenyan international striker Taiwo Atieno, who started his career when Money was manager of Walsall and had most recently played football in the US, was signed on a free transfer until the end of the season.

[96] A ninth consecutive victory was assured two days later as Luton beat already relegated side Grays Athletic 6–0 at Kenilworth Road, with Kevin Gallen scoring the first hat-trick of his career.

[99] A 0–0 home draw on 17 April with Altrincham, coupled with Stevenage's victory over Kidderminster that led to them being crowned as Conference Premier champions, meant that Luton's only hope of promotion was now through the play-offs.

[101] Luton lost the first leg at Bootham Crescent 1–0, an 89th-minute goal from Richard Brodie leaving them having to win the return game to have any chance of playing in the final.

Four players – Steve Basham, Shane Gore, Asa Hall and Rossi Jarvis – were released from their contracts, while a further four – Gavin Caines, Liam Hatch, Craig Nelthorpe and Mark Nwokeji – left the club as their loan period had ended.

[105] Luton made their first signing of the season on 19 May, with Cambridge United defender Dan Gleeson making the move to Kenilworth Road on a free transfer.

Striker Danny Crow, who had finished the season as Cambridge United's top scorer, signed on a free transfer on 21 May, penning a two-year contract.

[108][109] On 27 May, Luton announced they were to sign Stevenage midfielder Andy Drury, who had played 30 league games during the season as the club claimed the Conference title, on a two-year contract beginning from 1 July 2010.