Bolton began their pre-season games at Ayr United where they drew 1–1, Marcos Alonso scoring midway through the second half before Mark Roberts equalised for the home side.

Falkirk striker Lyle Taylor scored after just fifteen seconds, lobbing Ádám Bogdán, with Chris Eagles equalising 14 minutes later.

Crewe took the lead on thirteen minutes through Max Clayton, but Bolton equalised when Martin Petrov converted a penalty midway though the first half.

Afobe made his second appearance for the club, and scored a hat trick, in Bolton's penultimate pre season game, as they beat Tranmere Rovers 3–1, Jean-Louis Akpa Akpro replying for the home team.

The home side, playing their only pre-season game at The Reebok Stadium, twice came from behind, Marvin Sordell and a Sergi Gómez own goal cancelling out efforts by Cristian Lobato and Iván Balliu.

Forest took the lead when Lewis McGugan scored from 30 yards out, but Eagles equalised shortly before half time after a Kevin Davies header came back off a post.

Marvin Sordell gave Bolton the lead four minutes into the second half, before Andy Reid equalised for Forest, the game finishing as a 2–2 draw.

[5] Bolton began September away at Hull City on the first day of the month and took the lead through Chris Eagles' third goal of the season, a thirty five yard free kick.

An early Leroy Lita goal was cancelled out by Chris Eagles just before half time, but Marlon King scored from the penalty spot soon after the restart to give the home side the win.

The win took Bolton up to thirteenth position, but they failed to capitalize on this victory by losing 1–0 at home to Crystal Palace the following Saturday, Glenn Murray scoring the only goal of the game from the penalty spot after Zat Knight had fouled Wilfried Zaha.

The home side took the lead through Darius Henderson midway through the first half but Chris Eagles equalised early in the second before missing a penalty.

Martin Petrov converted the penalty to equalise and then Ngog himself scored in the 74th minute to give Bolton a 2–1 lead before being sent off in stoppage time for a second bookable offence.

Ádám Bogdán saved a penalty from Brighton's Ashley Barnes in the first half and the home side also hit the post three times.

Jordan Rhodes pulled one back for Blackburn with eight minutes to go, but Bolton held on to claim their second away win of the season and remained in the same position in the league.

After falling behind to a Nikola Žigić header after 11 minutes, Bolton equalised and then pulled ahead before the first half was over through goals from Marcos Alonso and Lee Chung-yong, respectively.

Bolton started 2013 with a loss at Leeds United, a solitary goal scored by Luciano Becchio from the penalty spot being the difference.

The match ended goalless, securing Bolton's first clean sheet in the league since the opening day of the 2011–12 season, as they spent the whole of the month in 16th position.

The game saw Marvin Sordell's first return to his former club since leaving the previous year and it was the former Watford man who opened the scoring through a penalty midway through the first half.

The match finished level despite Marcos Alonso being sent off for two bookable offences with ten minutes remaining to prevent returning Forest manager Billy Davies from starting his second spell in charge with a win.

After Craig Dawson's third goal in two games in the fifth minute, Bolton hung on for a slender victory, sending them to a season-high of tenth in the table.

Bolton's unbeaten streak came to an end against Ipswich Town at Portman Road, losing 1–0 to a late Carlos Edwards goal and leaving them five points off the play-offs going into the international break.

After initially going 2–0 up through Marvin Sordell and Medo's first for the club, Charlton hit back with three of their own, two of which came after Sam Ricketts was sent off for a second bookable offence.

Bolton looked to extend their home winning streak to six games and they succeeded in this endeavor courtesy of a Chris Eagles goal in the second half.

Two goals in the first ten minutes from David Ngog and Marcos Alonso and no reply from Wolves ensured they obtained the win and a fifth successive clean sheet at home.

Following this result, Bolton dropped to seventh place with Leicester City taking the vacated final play-off spot.

Middlesbrough equalised with a header from Kieron Dyer but three minutes later, Darren Deadman awarded a penalty to Bolton after Jonathan Woodgate brought down Lee Chung-yong.

Needing a win to all but confirm a play-off place,[15] Bolton fell behind to goals from Matt Phillips and Ludovic Sylvestre, while Nottingham Forest and Leicester City were drawing 1–1.

Bolton took a 2–0 lead with goals from Lee Chung-yong and Marvin Sordell, but Sunderland fought back for a draw through Connor Wickham and Craig Gardner, meaning there will be a replay at the Stadium of Light.

However, in the first minute of stoppage time, substitute John Heitinga scored from the edge of the penalty area to send Bolton out of the FA Cup.

Another reserve team striker, Jack Sampson, joined Accrington Stanley on a one-month loan deal on 11 October.