The 23-year-old was arrested at his home in the early hours of Tuesday after a man alleged he had been “tied up, beaten and held by Semedo and two other men at the player’s villa in Betera”, near Valencia, Las Provincias newspaper said.
Villarreal later issued a statement saying they had opened disciplinary proceedings against the player to investigate what had happened.
Semedo, who was remanded in custody when he appeared in court on Thursday, is also accused of assault and battery, threats, illegal possession of weapons and theft with violence, said a justice spokesman.
His court appearance came just hours before his team played a Europa League game at home to Lyon which they lost.
Las Provincias reported that the alleged victim was locked in a bedroom while the men took the key to his apartment in order to “rob money or get hold of something that could have held them responsible for another offence”.
It is not the first time Portuguese under-21 international Semedo has been in trouble with police since signing for Villarreal from Sporting Lisbon prior to this season.
He was arrested in November following an alleged altercation at a nightclub, for which he is awaiting trial.