Following a mixed first season in charge of the club, manager Roberto Martínez decided to make several additions to the playing squad. Wigan's most expensive summer signing was Argentine striker Mauro Boselli, who signed for an undisclosed fee believed to be in the region of £6 million. Dutch defender Mario Melchiot and Austrian midfielder Paul Scharner both left the club after their contracts expired. Gary Caldwell was named as the new club captain.
Wigan's first pre-season friendly was a 3–2 win against Östersunds FK, with new signing Boselli scoring twice. Their next friendly was a 1–1 draw against Oldham Athletic, featuring trialists Laurent Merlin and Sekou Baradji. Baradji also joined the squad at their pre-season training camp in Austria, but would ultimately not be offered a contract.
After an international break, Wigan's first game of the month was against Sunderland, which saw Lee Cattermole and Titus Bramble appear at the DW Stadium for the first time since leaving Wigan. Despite Cattermole being sent off in the first half, Wigan failed to capitalise on their man advantage and drew the match 1–1. The Latics then slipped into the bottom three after a 2–0 home defeat to Manchester City in the following game. The club progressed once again in the League Cup, winning the match 2–1 after a late comeback against Preston North End. The club finished the month with a goalless draw at Birmingham City.
On 2 October, Wigan Athletic picked up their first Premier League home win of the season after defeating Wolverhampton Wanderers 2–0. Two weeks later, the club drew 2–2 away against Newcastle United, with Charles N'Zogbia scoring both goals for Wigan against his former club. Wigan extended their unbeaten run with a 1–1 draw at home against Bolton Wanderers, but midfielder James McCarthy suffered an ankle injury which kept him out of action until the end of January. In the following game however, Gary Caldwell returned to the line-up for the first time since his hip operation during the summer as the team reached the quarter-finals of the League Cup following a 2–0 victory against Swansea City. On 30 October, Wigan were beaten 2–0 by Fulham.
Wigan started the month with a second away defeat in a row, losing 2–1 to Blackburn Rovers. Results then improved in their following two home games with a 1–1 draw against Liverpool and a 1–0 win against West Bromwich Albion. The club lost 2–0 in its next match against Manchester United, finishing the match with nine men after Antolín Alcaraz and Hugo Rodallega were sent off. Two more away defeats followed, against West Ham United and Arsenal in the quarter-final of the League Cup, during which Victor Moses dislocated his shoulder, meaning he would be out of action for three months.
Wigan came from behind twice to draw 2–2 with Stoke City in their first game of the month. The team then extended their unbeaten run with a draw against Everton, a win against Wolverhampton Wanderers and another draw with Arsenal. On 31 December, the club completed the signing of Adrián López on a free transfer.