There is some debate as to what happened to Phone Guy's body after he was attacked. While it's entirely possible his body is nowhere in the pizzeria anymore, there are two leading theories as to what happened to it.

Chica's Suit Edit

By far the most popular theory is that Phone Guy was stuffed into Chica's suit when he was caught. The reasoning for this is, in certain poses when Chica opens her mouth, one can see an extra set of teeth inside her mouth. Judging by Phone Guy's call on the first night, the only human remains to see the light of day after putting the suit head on would be your eyes and teeth. However, Chica's second set of teeth look unrealistic and are most likely from her endoskeleton. Also, Phone Guy explicitly states that the animatronics will try to stuff you in a Freddy Fazbear suit. Finally, Chica already has an endoskeleton inside of her; it wouldn't make sense for the animatronics to stuff a human inside of her.
Another reason people think that Phone Guy is inside of Chica is because she makes raspy, human-like groaning noises when she's inside of The Office. However, Bonnie makes these noises also. A logical explanation for this would be that their artificial voice boxes (since they're singing animatronics, they most likely have one) are malfunctioning and need to be repaired. Considering that the company is rather stingy and wouldn't jump at the idea of hiring a repairman, and that the animatronics been singing these songs non-stop for 20+ years, it makes sense that their voice boxes would get damaged from repeated use.

Golden Freddy's Suit Edit

Another popular theory is that Phone Guy was stuffed into the Golden Freddy suit. This seems plausible, as when Golden Freddy appears in The Office, he takes the position of a slumped over corpse. Adding to it, an endoskeleton cannot be seen inside Golden Freddy, especially since he has no eyes. This also lines up with the fact that Golden Freddy is a Freddy Fazbear suit, making it a very likely candidate to be stuffed with a security guard.