The new Owls boss oversaw a stoppage time defeat against 10-man Rotherham United on Wednesday evening – a result that leaves Wednesday seven points from safety and winless in their last five outings.
By contrast, have arrested a wobble of their own in recent weeks with back-to-back 1-0 wins over Rotherham and Blacburn Rovers.
The Royals are currently fifth in the table, six points off the automatic promotions spots.
Looking ahead to Saturday’s match, Prutton believes that they will dole out more misery for Wednesday too.
Speaking to Sky Sports News, he said: “Back-to-back wins for Reading this week, which they needed considering the charge of some of the sides below them.
"They are bubbling along nicely in the spot they are in.
“Sheffield Wednesday are in a spot of trouble. Darren Moore came in, but it's not the first result he would have wanted against Rotherham.
"I think it could well be another defeat on Saturday for him and his side.”
Prutton predicts a 2-1 Reading win.
The last meeting between these two sides ended in a 1-1 draw back in December, with Lucas Joao cancelling out an early strike from Callum Paterson at Hillsborough.
Wednesday haven’t beaten the Royals since August 2019, when they recorded a 3-1 victory at the Madejski Stadium.
Joao was on the scoresheet for the Owls that day, as were Kadeem Harris and Sam Hutchinson.