Signed as a winger from Vancouver Whitecaps in January last year, the Canada star has developed into one of Europe's best left-backs this season and earned a contract extension until 2025.
The 19-year-old's form has helped Bayern to sustain their challenge for the treble in 2019-20, and Flick has no doubt he can get even better.
"Alphonso is doing outstandingly at the moment," Flick said. "In addition to his speed on the pitch, he's very adept defensively.
"Now, he's setting up goals in attack and has scored some himself. He's on a very good path. He's young - he can and wants to learn.
"Despite his young age, he's currently one of the top performers."
Bayern face Eintracht Frankfurt on Wednesday, against whom they lost the 2018 final, but their 11-game winning run in all competitions places them as firm favourites to progress.
They beat Frankfurt 5-2 last month in the Bundesliga, too, although Flick is not prepared to underestimate their opponents.
"We approach the game like all the others," he said. "We are analysing Frankfurt for the third time in a season.
"We have to be very focused over 90 minutes, or longer in the cup. The team know about Frankfurt's strengths but also know about their own."
Another Bayern player to enjoy strong form since German football returned last month is Leon Goretzka, who got a goal and an assist in last Saturday's 4-2 win at Bayer Leverkusen.
Flick thinks the midfielder reflects the positive team spirit within the squad.
"He has a healthy aggression and so wins the ball a lot, and then he can start dangerous attacks," he said.
"But I don't want to single out one man. The whole team is excellent off the ball and also with the ball. Everyone feels a responsibility without the ball, and everyone wants to support each other with it.
"Not having an atmosphere [in behind-closed-doors games] may also help, since we speak a lot with each other. You can tell on the bench how everyone is, too – they also want to support. I like that. It shows the team spirit."