In the 2015–16 season, Trotter made one appearance for the side in the opening game of the season against Derby County before suffering a hamstring injury shortly after. Shortly after, he was placed available on loan, as his first team opportunities was limited under the management of Neil Lennon. After returning from a loan spell at Nottingham Forest, he returned to the club's first team, coming on as a late substitute, in a 1–1 draw against Eastleigh in third round of the FA Cup on 9 January 2016. Trotter started against Eastleigh in the third round replay of the FA Cup and helped them beat Eastleigh 3–2 to progress to the next round. Since returning to the first team, he regained his first team place for the side, playing in the midfield position. His return to the first team had convinced Manager Lennon that he was wrong to leave out Trotter. However, he suffered a hamstring injury during a 2–1 win over Rotherham United on 6 February 2016 and had to be substituted. It wasn't until on 5 March 2016 when Trotter returned to the starting line-up, coming on as a substitute in the 68th minutes, in a 2–1 loss against Leeds United. He then scored his first goal of the season, in a 2–1 loss against Preston North End, seven days later on 12 March 2016. After the match, Trotter said about the club's recent situation, saying: " We think about the fans because they pay a lot of money to watch us. They have put their cash into this club over the years and no-one knows where it has gone. The club is in a bad financial state. They have the most right to be upset because their money has been misused. Of course we feel for them. They have been very understanding and have supported us through every single game. Since I have been back, this was probably the first time we've been booed. It is a credit to them. This isn't for us, we need to keep going for them." Following a 3–1 loss against Brentford on 6 April 2016, Trotter caused controversy along with David Wheater when they made "an abusive finger gesture" on camera; which he apologised afterwards. As a result, the pair was disciplined by the club. Shortly after, Bolton Wanderers was relegated to League One after losing 4–1 to Derby County on 9 April 2016. Soon after, Trotter was dropped from the first team and never played again for the rest of the season. At the end of the 2015–16 season, Trotter went on to make sixteen appearances and scoring once for the season.
Trotter started the 2016–17 season well when he scored his first goal of the season, in a 2–1 win over AFC Wimbledon on 13 August 2016. Trotter then continued to establish himself in the starting eleven for the side, playing in the midfield position. Trotter started every matches since the start of the season until he was placed at the substitute bench at the beginning of October. After returning to the starting line-up against Port Vale on 29 October 2016, he scored his second goal of the season, in a 1–0 win over Grimsby Town in the third round of the FA Cup. But Trotter suffered an injury and suspended for picking up his fifth booking this season. After missing seven matches, he made his return to the first team on 2 January 2017, in a 2–2 draw against Coventry City. During the match, Trotter was substituted in the 59th minutes, lead the club's supporters to cheer sarcastically. His second goal for the club then came on 11 February 2017, in a 4–1 win over Walsall. However, by mid–March, he was dropped from the starting line–up and never played for the team again. Despite this, Trotter was part of the team that saw Bolton Wanderers promoted to the Championship after spending one season at League One.