Mr Bercow met with one complainant, a Westminster worker, who told him Nigel Evans had placed his hand in his boxer shorts while he was asleep at the Ribble Valley MP's home in 2009.
Last April's meeting in the Speaker's study was set up by Tory MP Dr Sarah Wollaston after the complainant confided in her the month before.
A second alleged victim told Dr Wollaston he had been raped by Mr Evans at his Lancashire home last year.
The court heard Mr Bercow agreed "in principle" to also meet the rape complainant but that was cancelled following legal advice - partly because it was said to have taken place outside the parliamentary estate.
In a witness statement read out at Mr Evans's trial at Preston Crown Court, Mr Bercow said he was contacted by Dr Wollaston, the MP for Totnes, who wished to see him on a matter of "some urgency".
He was later told by Dr Wollaston that it had been brought to her attention that two people had said they were raped and sexually assaulted by Mr Evans.
Mr Evans denies one rape, two indecent assaults and six sexual assaults. The trial continues.