The 25-year-old spent the second half of last season on loan at the Reebok Stadium, scoring one goal in 16 games.
Trotter, who will officially join Bolton on July 1, has signed a three-year contract with the Championship side.
The midfielder leaves Millwall following a four-year spell at The Den.
Bolton recently finished in 14th place in the Championship table.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| C | Leicester CityLeicester | 46 | 31 | 4 | 11 | 89 | 41 | 48 | 97 |
| P | Ipswich TownIpswich | 46 | 28 | 12 | 6 | 92 | 57 | 35 | 96 |
| 3 | Leeds UnitedLeeds | 46 | 27 | 9 | 10 | 81 | 43 | 38 | 90 |
| 4 | Southampton | 46 | 26 | 9 | 11 | 87 | 63 | 24 | 87 |
| 5 | West Bromwich AlbionWest Brom | 46 | 21 | 12 | 13 | 70 | 47 | 23 | 75 |
| 6 | Norwich CityNorwich | 46 | 21 | 10 | 15 | 79 | 64 | 15 | 73 |
| 7 | Hull City | 46 | 19 | 13 | 14 | 68 | 60 | 8 | 70 |
| 8 | Middlesbrough | 46 | 20 | 9 | 17 | 71 | 62 | 9 | 69 |
| 9 | Coventry CityCoventry | 46 | 17 | 13 | 16 | 70 | 59 | 11 | 64 |
| 10 | Preston North EndPreston | 46 | 18 | 9 | 19 | 56 | 67 | -11 | 63 |
| 11 | Bristol City | 46 | 17 | 11 | 18 | 53 | 51 | 2 | 62 |
| 12 | Cardiff CityCardiff | 46 | 19 | 5 | 22 | 53 | 70 | -17 | 62 |
| 13 | Millwall | 46 | 16 | 11 | 19 | 45 | 55 | -10 | 59 |
| 14 | Swansea CitySwansea | 46 | 15 | 12 | 19 | 59 | 65 | -6 | 57 |
| 15 | Watford | 46 | 13 | 17 | 16 | 61 | 61 | 0 | 56 |
| 16 | Sunderland | 46 | 16 | 8 | 22 | 52 | 54 | -2 | 56 |
| 17 | Stoke CityStoke | 46 | 15 | 11 | 20 | 49 | 60 | -11 | 56 |
| 18 | Queens Park RangersQPR | 46 | 15 | 11 | 20 | 47 | 58 | -11 | 56 |
| 19 | Blackburn RoversBlackburn | 46 | 14 | 11 | 21 | 60 | 74 | -14 | 53 |
| 20 | Sheffield WednesdaySheff Weds | 46 | 15 | 8 | 23 | 44 | 68 | -24 | 53 |
| 21 | Plymouth ArgylePlymouth | 46 | 13 | 12 | 21 | 59 | 70 | -11 | 51 |
| R | Birmingham CityBirmingham | 46 | 13 | 11 | 22 | 50 | 65 | -15 | 50 |
| R | Huddersfield TownHuddersfield | 46 | 9 | 18 | 19 | 48 | 77 | -29 | 45 |
| R | Rotherham UnitedRotherham | 46 | 5 | 12 | 29 | 37 | 89 | -52 | 27 |
| > Championship Full Table | |||||||||
