the start of the 2016–17 season saw baldwin being booked for the first three league matches before being sent-off for a second bookable offence, in a 2–1 loss against oxford united on 20 august 2016. after serving a one match suspension, since the start of the season, baldwin featured in every league matches until he was demoted to the substitute bench for two matches due to good performances from ryan tafazolli. however, he suffered a knee injury that kept him out for two months. it wasn't until on 21 february 2017 when baldwin returned to the first team and captained the side as well, in a 4–1 loss against southend united. four days later, on 25 february 2017, baldwin captained and scored again, in a 3–1 win over rochdale. despite being absent on two occasions later in the season, baldwin finished the 2016–17 season, making twenty-nine appearances and scoring once in all competitions. on 25 may 2017, baldwin signed a new two-year contract with the league one side.