The Braunschweig state court on Tuesday acquitted the 47-year-old German national, who has been identified by local media as Christian Brueckner, of two counts of rape and two of sexual abuse.
However, Brueckner will remain in prison another year because he is still serving a seven-year sentence for rape in a different case, German news agency DPA reported.
Brueckner had been on trial since February over offences he is alleged to have committed in Portugal between 2000 and 2017.
Defence lawyers had pointed to what they labeled a lack of evidence and witnesses who were not credible, and suggested he might not have been charged if he had not also been a suspect in the McCann case.
Christian Brueckner is under investigation on suspicion of murder in the Madeleine McCann case. (AP PHOTO)
Prosecutors had argued he should be given a 15-year prison sentence and kept in preventive detention once he has served it.
The verdict can be appealed.
Brueckner has not been charged in the McCann case, in which he is under investigation on suspicion of murder.
He spent many years in Portugal, including in the resort of Praia da Luz around the time of Madeleine's disappearance there in 2007.
He has denied any involvement in her disappearance.
He is serving a seven-year prison sentence after being convicted in 2019 by the Braunschweig court for the rape of a 72-year-old American woman in Portugal in 2005.
The Braunschweig state court has jurisdiction because Brueckner had his last German residence in that city in Lower Saxony.
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