The Portuguese manager has made quite an impression during his short stay at the Tigers, but he couldn't avoid them suffering relegation to the Championship last week.
He originally signed on a deal until the end of the season, and that has left the Tigers vulnerable to losing him over the summer.
Maloney said: "The manager did an unbelievable job to give us a chance to stay up.
"Him coming in in January gave us hope which I don't think we had the right to have, but he gave us that, dragged us through and signed some players that improved the squad.
"He's an excellent manager. I'm sure the owner will speak to him in the next couple of days and those discussions we aren't privy to. But he has been excellent for us and has been a real pleasure to work for.
"I would imagine the club would be absolutely desperate to keep him."