[1] The deal sparked protests from fans and local politicians alike, with a petition asking the club to rethink the decision reaching over a thousand signatures within just over twenty four hours.

[3] On 5 June 2013, Bolton announced that they would no longer be entering into a sponsorship agreement with QuickQuid due to "the adverse reaction to the sector of business in which the sponsor operated".

After travelling to the south of Spain for a week-long training camp on 7 July 2013, Bolton returned to play against Rotherham United, a game they lost 2–1 despite taking the lead through Marvin Sordell.

At a fans' forum held at the Reebok Stadium on 29 July, manager Dougie Freedman confirmed that Zat Knight had been made team captain for the forthcoming season.

[6] On the same day, the club website confirmed that Stuart Holden had torn his anterior cruciate ligament in his right leg while playing for the United States in the CONCACAF Gold Cup final against Panama.

Darren Pratley got his second goal in as many league games to put Bolton in the lead, but Reading equalised through a Nick Blackman penalty early in the second half.

The loss, Bolton's fourth in a row, left them winless in the new season, though they moved off the foot of the table courtesy of Millwall's poorer goal difference.

Despite halting their four-game losing run with a 2–2 draw in their next game against Derby County, Bolton slipped to the bottom of the table again as Millwall beat Blackpool.

Yeovil took the lead after 'keeper Ádám Bogdán spilled an Ed Upson shot before Alex Baptiste headed in his third goal of the season in the 90th minute to equalise and push Bolton off the foot of the table, with Barnsley dropping below them.

Striker Jermaine Beckford hit the woodwork, while Kevin McNaughton and Neil Danns made their debuts and Liam Feeney earned his first start, but Bolton could not break the deadlock and the game finished 0–0, giving Bolton just their third clean sheet away from home since their win against QPR on the opening day of the 2011–12 season and ending Blackpool's season-long run of scoring in every match.

After taking the lead through a free-kick taken by Medo Kamara, David McGoldrick equalised for Ipswich, leaving Bolton five games unbeaten but just one place above the relegation zone.

Bolton's next game against Millwall extended that run with their first home win of the season as Robert Hall, Jermaine Beckford and André Moritz all scored past David Forde in a 3–1 victory.

On the final day of November, Bolton travelled to the Riverside Stadium to face Middlesbrough for new manager Aitor Karanka's first home game for Boro.

Back at the Reebok Stadium against Huddersfield Town after an international break and two away matches, Bolton failed to capitalise on their previous home win against Millwall, falling to Oliver Norwood's second strike in two games, beating Andy Lonergan from 30 yards.

Bolton won against Barnsley on Boxing Day, with Neil Danns scoring in the last game of his loan spell, as he was unable to play against Leicester City, his parent club, that weekend.

Leicester took the lead through former United player Danny Drinkwater before goals from André Moritz and Jermaine Beckford turned the tie in Bolton's favour.

Adam Le Fondre scored a first half hat-trick within 33 minutes, before Pavel Pogrebnyak added a fourth after Alex Baptiste handled in the box to concede a penalty.

Bolton lost for the third time running in all competitions, going down 2–1 to QPR at Loftus Road, Jay Spearing scoring his first of the season via a deflection in the last ten minutes.

Medo Kamara opened the scoring with a placed header, having been set up by Neil Danns' cross before Joe Mason doubled the lead with his second strike in as many games shortly before half-time.

Powell proceeded to score on the 88th minute, firing home from Martyn Waghorn's cross, while Baptiste conceded a second penalty in two games, forcing Ádám Bogdán to rescue the point for Bolton; saving Jordi Gómez's spot-kick high to his right.

Bolton continued their winning streak against Barnsley; Jermaine Beckford rounding the 'keeper after getting on the end of a Matt Mills long ball on the stroke of half-time.

On 22 April, Leicester City won the Football League Championship at the Reebok Stadium; winning 1–0 – a Lloyd Dyer strike giving them the result they needed.

Away at Hillsborough on 26 April, Bolton raced into a three-goal lead courtesy of goals from Neil Danns, Lee Chung-Yong and Liam Trotter's first for the club.

[18] Substitute Fraizer Campbell scored just after half-time for the Bluebirds to send Bolton out of the FA Cup; who exited at the fourth round for the second consecutive year.

Making his full debut for the club, academy graduate Sanmi Odelusi then scored two goals either side of half-time to put Bolton 3–1 up.

Adam Blakeman, who made a senior appearance against Macclesfield Town in the League Cup, Alex McQuade, Jack Sampson, Joe McKee and goalkeeper Lewis Fielding were all released.

On 14 May, it was announced that Bolton had signed two teenagers to add to their academy; 17-year-old Sheffield Wednesday full-back Hayden White and 18-year-old Millwall forward Conor Wilkinson.

The first incoming player of the loan transfer window for Bolton was Leicester City midfielder Neil Danns, who was brought in on a three-month deal.

Although Hayden White, Conor Wilkinson and Robert Hall were signed by Bolton after their contracts had run out, Sheffield Wednesday, Millwall and West Ham, respectively, would be entitled to compensation as the players were under the age of 23.

On 21 March, Josh Vela was sent on loan to Notts County, who were bottom of League One and managed by Dougie Freedman's former Crystal Palace teammate Shaun Derry.