Federer beat David Goffin to reach the quarter-finals earlier today before Zverev followed him into the last eight with a straight-sets victory over Andrey Rublev.
The last time Federer and Zverev met, the 20-time Grand Slam champion was giving his team-mate advice during the Laver Cup.
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But now they will play in an outdoor hard-court tournament for the first time in more than two years and Zverev is expecting the Swiss, whom he has beaten three times in six meetings, to provide a unique challenge.
"I think it was very good tennis [against Rublev]," Zverev said.
"But I know against Roger it's going to be very, very difficult.
"He's going to try to do different things, and it's going to be a difficult match."
Zverev has one of the best active records around against Federer, having beaten him on the grass of Halle, the hard courts of Montreal and under the roof of the O2 Arena.
But the 22-year-old has never made it past a Grand Slam quarter-final and is one of the new generation of players whom Federer himself believes will eventually surpass those at the top, even if they have not yet.
"I am seeing big improvements now," Federer said.
"Not like there were none beforehand, but now they are playing with the big boys and really able to challenge us, beat us, having good rivalries also within each other, which I think is important for them to improve as players.
"So I think it really creates good intentions to actually wanting to improve faster, and I see that right now.
"Each one of them has really shown some really good matches and some great runs."
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