Police had been searching for the severely disabled 14-year-old for the last month when he was found in the man’s apartment in Lübbenau, Brandenburg, on Friday.
The man, whose 13-year-old daughter sometimes lived with him, was arrested.
Cottbus prosecutor Petra Hertwig said on Sunday the boy had been sexually abused and the divorced taxi driver is being investigated for 175 cases of child abuse stretching back 20 years.
According to prosecutors, the 14-year-old knew the man and when he went missing four weeks ago after he went to his home.
Prosecutors repeatedly visited the 52-year-old’s home over the period to question him about the disappearance of the boy, but never saw the teenager because he hid behind a cupboard when they came round.
“What happened in the apartment is only gradually coming to light,” police said.
The man is accused of molesting 100 children and 75 adolescents.