Christian Brueckner is accused of attacking five women and girls in Portugal between 2000 and 2017.
These charges are separate from the murder inquiry linked to Madeleine's disappearance, which is ongoing.
But prosecutors in Braunschweig, northern Germany, said on Tuesday that the suspect was the same man.
Madeleine, then aged 3, disappeared from a holiday villa in Praia da Luz, southern Portugal, in May 2007. The case gripped the British public and media, but she was never found.
Authorities in Germany announced in 2020 that they had identified a new suspect, later revealed to be Brueckner, a German national with former addresses in Portugal and a history of sexual offences.
He denied involvement in Madeleine's disappearance and no charges have been brought.
Prosecutors separately took up inquiries into the alleged sexual offences in Portugal. They were investigated in Braunschweig because Brueckner's last known address in Germany was in the city.
Brueckner, who is in prison in Oldenburg, north-west Germany, for a separate rape conviction, faces three new counts of rape and two of sexual assault.
Two of the alleged victims were a German girl of 10 and a Portuguese girl of 11, prosecutors said.
The others were a German-speaking girl of about 14, an Irish woman, 20, and a woman aged between 70 to 80.
A 100-page indictment was filed after "very intensive" investigations in several European countries over a period of years, German authorities said.