On 29 May, the club announced a new shirt sponsorship deal with pay day loan company QuickQuid, replacing 188BET who sponsored the club's shirts for the previous two seasons. 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.Bolton South EastMP, Yasmin Qureshi, called the deal "completely wrong" and joined fellow local MPs David Crausby and Julie Hilling, alongside Bolton Council leader Cliff Morris and Bolton at Home chief executive Jon Lord in calling upon the club to reconsider the decision.
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". In the same announcement, Bolton announced that their new shirt sponsor would be FibrLec, who work with the town's university.
On 17 May 2013, Bolton announced a total of eight pre-season fixtures split between the first team and a Bolton XI. 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. They next played Shrewsbury Town, to whom Tom Eaves was on loan towards the end of the 2012–13 season. The game ended in a 3–3 draw, with a Sordell brace and a goal from Chris Eagles. The penultimate game was at Carlisle United where Bolton lost 1–0 after an early goal. Bolton announced their home pre-season friendly on 3 June 2013, facing Real Betis on 26 July at the Reebok Stadium. Bolton lost their final pre-season friendly 2–0 courtesy of goals from Jorge Molina and Joan Verdú either side of half-time.
A Bolton XI played against Skelmersdale United, winning 1–0 through a Josh Vela penalty. The development squad also played against Chorley for the Harold Taylor Memorial Trophy. Bolton won 2–1 with goals from new signing Gary Fraser and Tom Youngs. This was followed by a match against F.C. United of Manchester at Bury'sGigg Lane. The game ended in a 1–1 draw with Conor Wilkinson grabbing Bolton's goal. The development squad's next game of pre-season came away at Chester. With first team players such as Craig Davies, Tyrone Mears and Matt Mills featuring, Bolton could only secure a stalemate at the Exacta Stadium. The squad's penultimate pre-season game finished with a win for the Whites as a Tom Eaves in the second half settled the affair. The Bolton XI finished their pre-season preparations with a win over Stockport County at Edgeley Park.
The fixtures for the 2013-14 Football League Championship season were released on 19 June 2013. However, on 18 June the Football League announced six opening day fixtures, all involving the eight founder members who are currently playing in the Football League, as part of the league's 125th anniversary celebrations.
For the second consecutive season, Bolton visited fellow founder members Burnley at Turf Moor on the opening day of the season. After falling behind to a Danny Ings shot that deflected off David Wheater in the 26th minute, the goal eventually being given to Ings by the Football League, Bolton equalised through Darren Pratley in the 37th minute. No further goals were scored to give Bolton a draw in their first match of the season. Bolton's first home game of the season was against relegated Reading. 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. On 17 August Bolton travelled to the City Ground to face Billy Davies'Nottingham Forest. Bolton conceded after two minutes to a Jamie Mackie goal, which was followed by two further goals in the second half for Nottingham Forest to hand Bolton their first defeat of the season, with Darren Pratley being sent off during the match. Bolton's second home game of the season came against QPR, who had been relegated from the Premier League the previous season. The game was preceded by the unveiling of a statue of Nat Lofthouse outside the Reebok Stadium. After a goalless first half, QPR edged ahead through Andy Johnson in the 54th minute. This was Bolton's first home loss in 2013, ending a 12-game unbeaten home run, and left them without a win in the new season. Bolton's winless run continued against local rivals Blackburn Rovers at Ewood Park, where they fell to a 4–1 loss. This left Bolton at the foot of the table going into September.
At home to Leeds United, Bolton conceded to an early Luke Varney goal from a corner and failed to respond; with Bolton registering only one shot on target throughout the match. 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. DefenderAlex Baptiste scored his second goal of the season to put Bolton ahead on five minutes before Johnny Russell scored two to put Derby in front. Chris Eagles equalised after forty minutes to earn Bolton the point. In their eighth match, Bolton faced Brighton & Hove Albion at the AMEX Stadium. After taking the lead through a Lee Chung-Yong cross that deflected off David López, Bolton went in at half-time a goal to the good. However, after conceding three goals in four minutes in the second half, Bolton left Brighton with no points. In their final game of September, Bolton faced the Glovers, Yeovil Town. Yeovil took the lead after 'keeperÁdám 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.
Aiming to finally get their first win of the season, Bolton kicked off at Blackpool'sBloomfield Road. StrikerJermaine 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 naming an unchanged side for the game against Birmingham City, Bolton took the lead with Jermaine Beckford's first league goal of the season before loanee Neil Danns scored against his former club to double the lead. Bolton were pegged back by substitute Nikola Žigić's header which looped over Ádám Bogdán, but held on to earn their first win of the season. Žigić's goal was later credited to Lee Novak. After the international break, Bolton played host to Sheffield Wednesday, the only team in the league without a win. Jermaine Beckford followed up his goal in the previous game by opening the scoring but Alex Baptiste put through his own net for Wednesday to equalise. In the last five minutes, Wednesday's José Semedo was sent off for a tackle on Jay Spearing but Bolton were unable to capitalise on the advantage as the match ended 1–1. The following match took place against Ipswich Town, with Bolton looking to win at home for the first time. 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.
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 Ollie Norwood's second strike in two games, beating Andy Lonergan from 30 yards. In an attempt to bounce back from the two consecutive defeats, Dougie Freedman made five changes from the team that fell at home to Huddersfield Town. André Moritz, who retained his place from the previous game, set up Joe Mason to score on his full debut before scoring himself from long range. Neil Danns wrapped things up in second half stoppage time to push Bolton back up to 15th place. Bolton faced Wigan on 15 December at the DW Stadium. As ex-Bolton manager Owen Coyle had been sacked by Wigan in the week preceding the match, new manager Uwe Rösler was looking to win in his first home game. Wigan were 2–0 up at half-time. They opened the scoring when Matt Mills was adjudged to have handled the ball in the box and Ben Watson subsequently dispatched the resulting penalty, before on-loan Nick Powell scored on 25 minutes. Bolton levelled 20 minutes after the break, their first goal coming four minutes after the restart, Neil Danns scorign his third goal for the club and the second came when Lee Chung-Yong was kicked in the penalty area, giving André Moritz the chance to put away the spot-kick for his third. However, just four minutes later, Wigan restored their lead through Callum McManaman to send Bolton home with no points. Bolton entered Christmas in 18th place thanks to a 1–1 draw with Charlton Athletic at the Reebok Stadium. They fell behind to a goal from Yann Kermorgant before equalising with Kevin McNaughton's first goal since 2008. 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. Bolton's final game of the year was a thrilling affair with eight goals being shared between the two sides. Bolton finished on the wrong end of the scoreline; with Leicester winning 5–3. 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. Leicester equalised when Anthony Knockaert scored but Moritz scored his second just a few minutes later. Leicester equalised a second time when Tim Ream deflected into his own net just before half-time. Leicester scored two more in the second half; Lloyd Dyer and Gary Taylor-Fletcher earning the three points for Leicester.
In their first home game of the new year, Bolton went 2–0 down in the first twenty minutes of the game against Middlesbrough. With nine minutes gone, Zat Knight lost the ball on the edge of the box, allowing Mustapha Carayol to played in. Following this, an error in communication between Knight and Andy Lonergan resulted in an over-hit backpass which let Curtis Main steal in to bag Middlesbrough's second. Alex Baptiste then scored his fourth goal of the season before half-time, and David N'Gog scored in the final minute of normal time to rescue the point for Bolton. In their next game, Bolton were thoroughly beaten by Reading at the Madejski Stadium. 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. The half-time scoreline was then nearly doubled; Kaspars Gorkšs, Hope Akpan and Nick Blackman making it seven. Sanmi Odelusi assisted David N'Gog's consolation goal, with two minutes remaining in the game. 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.
Bolton began the new month with another loss; to Ipswich Town at Portman Road. Andy Lonergan brought down David McGoldrick to concede a penalty which the striker also scored. Beginning a run of four home games in the next five, Bolton faced Bournemouth at home. Bolton obtained a two-goal lead in the first half-an-hour through Lee Chung-Yong's first of the season and Lukas Jutkiewicz's first for the club. However, Bournemouth replied almost immediately through Lewis Grabban before equalising from a corner; Simon Francis scoring the goal. Facing local rivals Burnley, also at home, Bolton fell to a second half goal from Sam Vokes. Following the game, Burnley manager Sean Dyche claimed that Bolton's match-day programme had partly inspired the win, saying, "I just took a few of the quotes and went up to a couple of them (Burnley players) and went 'apparently we're having a tough time'." They faced Millwall after this, at The Den. Despite taking the lead through Lukas Jutkiewicz in the 15th minute, as well as hitting the post from a Chris Eagles free-kick and missing a penalty which Jutkiewicz took, Bolton only returned with a point as Martyn Woolford equalised from a tight angle. Bolton started with two strikers in their next game against Watford, following Joe Mason's return to the club on loan. His strike partner Lukas Jutkiewicz scored his third goal in six games for the club before Mason scored on his second debut for the club, as he did against Doncaster earlier in the season. Bolton drew the second half to earn their third home win of the season.
Bolton made it two wins on the run in their first match of the new month, against local rivals Blackburn, who had beaten them 4–0 earlier in the season. Bolton made amends; winning 4–0 with two goals in either half. 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. Jay Spearing furthered the lead two minutes after the break; his long-range shot bouncing off the crossbar and over the line, leaving substitute André Moritz to finish the scoring with a low, powerful shot to Paul Robinson's right which the former England 'keeper couldn't keep out.
In news off the field, Stuart Holden was again injured after returning to playing duties in an U-21 match against Everton, against whom he completed only 23 minutes. On the Tuesday of the following week, it was announced that he would be out of the game again for between six and nine months following another operation on his knee.
Bolton travelled to the John Smith's Stadium to face Huddersfield Town in their first game of April. Both teams hit the woodwork in the first half via Danny Ward and Lee Chung-Yong for Huddersfield and Bolton, respectively, though the game looked as if it were headed for a scoreless draw until substitute Joe Mason scored in the second minute of injury time to push Bolton up to 15th in the table. Remaining in Yorkshire for another away match, Bolton faced Doncaster Rovers at the Keepmoat Stadium stadium on 8 April. Going two goals to the good in the first quarter of an hour, Doncaster halved the deficit when Wales midfielder David Cotterill put in a free-kick off the crossbar. No more goals were scored, leaving Bolton with two wins on the bounce and a six-match unbeaten away run. 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. Bolton couldn't continue their winning run in London; instead playing their part in a stalemate against Charlton Athletic at the Valley. It did, however, continue Bolton's seven game unbeaten away streak. 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. The score also ended Bolton's unbeaten run as they remained in 14th place. 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. Joe Mattock reduced the deficit for the home side but no further goals were scored to give Bolton their longest unbeaten away run since 2001; going eight games unbeaten.
Bolton will enter the FA Cup at the Third Round stage with the other Championship clubs, as well as those from the Premier League. On 8 December, Bolton were drawn to play Blackpool at the Reebok Stadium, with the match played on 4 January 2014. David N'Gog scored his second goal in as many games to open the scoring before Tom Barkhuizen scored just before half-time to level matters. The goal was initially ruled out for offside as a Blackpool player had impeded Andy Lonergan's view when in an offside position, but referee Simon Hooper overruled his assistant. Five minutes after the restart, however, N'Gog set up Jermaine Beckford to score his 17th goal in 20 FA Cup games, with the goal also meaning that he had scored in the 3rd Round of the FA Cup for the fifth season running, all for different clubs. The following day, Bolton were drawn against Ole Gunnar Solskjær'sCardiff City in the next round, again at home. 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.
On 7 May 2013, it was announced that seven academy graduates would not have their contracts renewed. 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 30 April 2013, it was confirmed that Alex McQuade had signed a one-year deal with Shrewsbury Town. A further announcement was made by the club website on 8 May 2013, detailing two more academy graduates who would be leaving; defenders Ben Dennis and Ben Hampson. It had previously been announced that club captain Kevin Davies would not be offered a new contract at the end of the preceding season. 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. On 20 May, it was announced that Bolton had signed out-of-contract left-backMarc Tierney from Norwich City. Bolton further bolstered their defence with the signing of another out-of-contract defender, Alex Baptiste, on 22 May. On 30 May, the signing of Marc Tierney was further confirmed by the club. On 31 May, it was confirmed that left-back Marcos Alonso had completed his move to Italian side Fiorentina. On 3 June, it was announced that ScottishwingerGregg Wylde had his contract terminated over the preceding weekend, making him a free agent. On 25 June, it was announced that 23 year-old goalkeeper Rob Lainton would not have his contract renewed making him a free agent. The following day, on Tuesday 26 June, released forwardJack Sampson signed a two-year deal with League Two side Morecambe. After his contract with Blackpool ran out on 30 June, the signing of Alex Baptiste was confirmed by the club on 1 July. Later the same day, Bolton confirmed the signing of West Ham winger Rob Hall on a three-year deal. Hall had been on loan to Bolton towards the end of the previous season. On 4 July, the club confirmed that defender Sam Ricketts' contract had been cancelled by mutual agreement. Later the same day, Wolverhampton Wanderers confirmed that they had signed the Walesfull-back on a free transfer. On 10 July, Bolton signed Gary Fraser, who had turned down an offer from the club in January, from Scottish outfit Hamilton Academical. This transfer was further confirmed by the club on 18 July. Former Leeds UnitedstrikerJermaine Beckford's protracted transfer from Leicester City was finally completed on 17 July. Bolton also signed 16 year-old Hungarian'keeper Erik Bukran from Budapest Honvéd. Although not confirmed by the club, Bukran appeared as a substitute in a Bolton XI's pre-season game against Chorley. As was previously thought, Gary Fraser was loaned out to Partick Thistle in the SPL on 22 July, for an initial six month period. On 1 August 2013, Bolton confirmed the free signing of BrazilianAndré Moritz on a one-year contract. Moritz had previously rejected a contract extension at his last club Crystal Palace. Shortly after it was confirmed that Marvin Sordell had moved to Charlton Athletic on a season-long loan. On 8 August, Bolton announced that former loanee Jay Spearing was having a medical with the club. The following day, Bolton's 2012–13 player of the year joined on a four-year contract. Released midfielderAdam Blakeman signed for non-league Hyde on 9 August. Following the arrival of Jay Spearing, fellow midfielderKeith Andrews was loaned to Brighton & Hove Albion for a season. Following on from Adam Blakeman's departure to Hyde, fellow academy graduate Ben Dennis also joined the non-league side.
On 11 November 2013, a deal was agreed with Premier League side Cardiff City to loan forward Joe Mason until 5 January 2014. However, the following day it was announced that Cardiff manager Malky Mackay had had a change of heart over the deal and the striker stayed in South Wales, despite having travelled up to Bolton to train with them on the previous day. The deal was finally completed on 27 November, with Mason signing until 5 January 2014. On 28 November, Craig Davies was set to move on loan to Wolves, before the deal fell through.