On 17 July 2012, Bolton Wanderers confirmed the signing of Lonergan on a three-year deal for an undisclosed fee.
Upon joining the club, Lonergan spoke about the challenge he was expecting to face at Bolton Wanderers.

His debut came on 28 August 2012 in a 2–1 defeat against Crawley Town in the League Cup second round.
However, Lonergan found himself competing with Ádám Bogdán over the first choice goalkeeper spot.
On 19 October 2012, Lonergan suffered a knee injury, which he sustained in training and was sidelined for two months.
Lonergan's first experience in front of the Reebok Stadium crowd was the 2–2 draw between Wanderers and Sunderland in which he was named Man of the Match for Wanderers following appreciation of his contribution following saves from Steven Fletcher on 5 January 2013 and played against them in the FA Cup third round replay on 15 January 2013, where he kept a clean sheet, in a 2–0 win to send them through to the next round.
Lonergan's first league game for Bolton came on 5 March 2013, as Bolton beat local rivals Blackburn Rovers by a single goal.
Lonergan made four more appearance and kept two more clean sheets before Bogdán returned from injury and went on to make eleven appearance in all competitions.

In the 2013–14 season, Lonergan continued to compete the first choice goalkeeper status with Bogdán, but was given an opportunity to make his first appearance of the season on 26 October 2013, in a 1–1 draw against Ipswich Town following Bogdán's injury.
After the match, Lonergan said he was happy to make his first appearance of the season.

From that moment on, Lonergan had become a first choice goalkeeper for the club from October to February.
He soon became at fault when he conceded five goals, in a 5–3 loss against Leicester City on 29 December 2013 and was even at fault further when he conceded ten goals in three matches against Reading, Queens Park Rangers and Ipswich Town.
Despite being reassured by manager Dougie Freedman that he would remain the first choice goalkeeper, Lonergan lost his first choice goalkeeper status to Bogdán and was on the substitute bench for the rest of the season until returning in goal, in a 2–2 draw against Birmingham City, which helped them survive relegation.
Lonergan went on to finish the 2013–14 season, making twenty–three appearance in all competition.

In the 2014–15 season, Lonergan made his first appearance of the season, but conceded three goals, in a 3–0 loss against Watford in the opening game of the season.
By the August, the club had rotate both Lonergan and Bogdán over the first choice goalkeeper role before Lonergan won the role and was the first choice goalkeeper for the most of the season, due to Bogdán's injury.
On 25 October 2014, Lonergan provided an assist for Craig Davies to score the third goal of the game, in a 3–1 win over Brentford.
Throughout December saw Lonergan making an impression, as he kept three clean sheets and won the Bolton Wanderers Player of the Month award for December.
Lonergan remained the first choice goalkeeper until he suffered a concussion after in the 65th minutes and was substituted as a result, in a 4–1 loss against Nottingham Forest on 21 February 2015 and said the concussion he sustained could have ended his career.
Despite being cleared from a serious injury after a scan, Lonergan lost his first choice goalkeeper status role following the arrival of Ben Amos and spent the rest of the season on the substitute bench.
Lonergan finished the 2014–15 season, making thirty–two appearance in all competitions.

On 10 June 2015, it was announced that Lonergan would leave the club upon the expiry of his contract.
During the match at Bolton Wanderers, Lonergan earned a cult status among Bolton Wanderers supporters and while playing, the supporters would chant for him to the tune of Simon and Garfunkel's Mrs Robinson: "And here's to you Andy Lonergan, Bolton loves you more than you will know..."
On 17 July 2012, Bolton Wanderers confirmed the signing of Lonergan on a three-year deal for an undisclosed fee. Upon joining the club, Lonergan spoke about the challenge he was expecting to face at Bolton Wanderers.
His debut came on 28 August 2012 in a 2–1 defeat against Crawley Town in the League Cup second round. However, Lonergan found himself competing with Ádám Bogdán over the first choice goalkeeper spot. On 19 October 2012, Lonergan suffered a knee injury, which he sustained in training and was sidelined for two months. Lonergan's first experience in front of the Reebok Stadium crowd was the 2–2 draw between Wanderers and Sunderland in which he was named Man of the Match for Wanderers following appreciation of his contribution following saves from Steven Fletcher on 5 January 2013 and played against them in the FA Cup third round replay on 15 January 2013, where he kept a clean sheet, in a 2–0 win to send them through to the next round. Lonergan's first league game for Bolton came on 5 March 2013, as Bolton beat local rivals Blackburn Rovers by a single goal. Lonergan made four more appearance and kept two more clean sheets before Bogdán returned from injury and went on to make eleven appearance in all competitions.
In the 2013–14 season, Lonergan continued to compete the first choice goalkeeper status with Bogdán, but was given an opportunity to make his first appearance of the season on 26 October 2013, in a 1–1 draw against Ipswich Town following Bogdán's injury. After the match, Lonergan said he was happy to make his first appearance of the season.
From that moment on, Lonergan had become a first choice goalkeeper for the club from October to February. He soon became at fault when he conceded five goals, in a 5–3 loss against Leicester City on 29 December 2013 and was even at fault further when he conceded ten goals in three matches against Reading, Queens Park Rangers and Ipswich Town. Despite being reassured by manager Dougie Freedman that he would remain the first choice goalkeeper, Lonergan lost his first choice goalkeeper status to Bogdán and was on the substitute bench for the rest of the season until returning in goal, in a 2–2 draw against Birmingham City, which helped them survive relegation. Lonergan went on to finish the 2013–14 season, making twenty–three appearance in all competition.
In the 2014–15 season, Lonergan made his first appearance of the season, but conceded three goals, in a 3–0 loss against Watford in the opening game of the season. By the August, the club had rotate both Lonergan and Bogdán over the first choice goalkeeper role before Lonergan won the role and was the first choice goalkeeper for the most of the season, due to Bogdán's injury. On 25 October 2014, Lonergan provided an assist for Craig Davies to score the third goal of the game, in a 3–1 win over Brentford. Throughout December saw Lonergan making an impression, as he kept three clean sheets and won the Bolton Wanderers Player of the Month award for December. Lonergan remained the first choice goalkeeper until he suffered a concussion after in the 65th minutes and was substituted as a result, in a 4–1 loss against Nottingham Forest on 21 February 2015 and said the concussion he sustained could have ended his career. Despite being cleared from a serious injury after a scan, Lonergan lost his first choice goalkeeper status role following the arrival of Ben Amos and spent the rest of the season on the substitute bench. Lonergan finished the 2014–15 season, making thirty–two appearance in all competitions.
On 10 June 2015, it was announced that Lonergan would leave the club upon the expiry of his contract. During the match at Bolton Wanderers, Lonergan earned a cult status among Bolton Wanderers supporters and while playing, the supporters would chant for him to the tune of Simon and Garfunkel's Mrs Robinson: "And here's to you Andy Lonergan, Bolton loves you more than you will know..."
Andy Lonergan