Bonnie makes an appearance in the second game Five Nights at Freddy's 2 with three other old animatronics.
In the second game, Bonnie has a very different design - like Freddy Fazbear, he also has two buttons on his chest. His face has been gutted, with most of it being removed, while his lower jaw remains, featuring more teeth than he possesses in the first game as well as glowing red irises. His left arm is missing entirely, with a mass of wires in its place.
His suit has become more tattered, particularly around the legs, and a few loose wires poke out of his body. The covering on his right hand and left foot have come off, revealing his endoskeleton. He also seems to have a bigger stomach, as it looks more rounded and bigger than his upper body. His chin also doesn't squash his bow tie now, and his suit seems to have changed to a darker shade of blue, as opposed to a lavender colour. It is explained in game that this new appearance is due to an attempted retrofit of the old animatronics that took place, before they got junked in favour of the Toy Models, such as Toy Bonnie.
Unlike in the first game, Bonnie appears to follow a fixed pattern, and no longer appears to teleport along his attack route. He starts moving at Night 2, but is very inactive until Night 3. Bonnie starts with the other old animatronics in the Parts/Service room and travels to the Main Hall. He then heads to the hallway outside The Office, staring at the player from just outside. After that, he travels into Party Room 1 to climb into the Left Air Vent in order to enter The Office, completely bypassing the Left Air Vent's blind spot.
When Bonnie is in The Office and either the player lowers their monitor or Bonnie forces it down, Bonnie will stand in front of the desk as the lights constantly flicker before he vanishes. The player has less than a second to put on the Freddy Fazbear Head the moment they see Bonnie to avoid imminent death. Delaying or neglecting to put the Head on will cause the screen to black out as normal, only for him to return and kill the player after bringing up and lowering the Monitor. He may also forcibly pull down the Monitor or remove the Freddy Head if left on some time after failing to ward him off.
Bonnie is incredibly active, especially on later nights; while he can be caught in the main hall, Bonnie can quickly move into The Office via the Left Air Vent, catching the player off-guard. Like the other animatronics, the Flashlight appears to make him wander off and/or slow him down.