Rooney has rediscovered something like his best form in recent weeks and he was again influential in United's 1-0 Premier League victory over Everton at Old Trafford on Saturday, drifting off the forward line expertly to dictate play.
Metzelder, 30, said Schalke are well aware of Rooney's ability to find space and would be looking to limit his freedom, even if merely seeking to do so and actually achieving that aim can be two different stories.
"It's all about stopping Rooney, he's the key player," Metzelder said. "The first match is at home so it will be very important not to concede a goal. Against Chelsea he dropped into the midfield, so it's important to defend against him not only with the defensive line but also with the midfielders.
Metzelder said he was glad Schalke had avoided favourites Barcelona in their first-ever Champions League semi-final, claiming United more conventional style of play is easier to counter than the tiki-taka of the Spanish pass-masters.
"Of course we know that Manchester United have so many key players but they don't scare us," he said. "It would be much more difficult for us to play against Barcelona. The style of Manchester United is easier for us, if you can say that. Barcelona take control and they make you run so much it's very difficult to defend against them. It's easier to play against teams like Manchester United - or even Real Madrid."
But Metzelder is by no means underestimating the challenge ahead for Schalke, though, conceding the German side are the underdogs.
"Manchester United have had so much experience in the Champions League over the last 20 years. Individually they are so very strong so they're big favourites.
"Our advantage is certainly that Manchester United will be busy thinking about facing either Real or Barcelona at Wembley in the final. We will definitely be looking to come up with something."