Boateng has started eight of Bayern's 17 Bundesliga matches this term and has been strongly linked with an exit in the January transfer window.
And stand-in boss Flick will let Boateng, who is out of contract at the end of next season, decide whether he stays on at the Allianz Arena or finds a new challenge elsewhere.
"I get along with him and we talk openly," Flick told German sports magazine Kicker.
"Against Wolfsburg he came into the side and had some problems, but then he showed he has the quality to play for Bayern.
"Jerome has to make the decision about his future because it's about his career."
Regardless of Boateng's future, Flick has set his sights on bringing in a new right-back in the coming weeks.
"Benjamin Pavard does well in every position but especially well at centre-back," he said. "Therefore an addition at right-back would be helpful.
"Winter transfers always bring something to a team if they help immediately - and this is difficult to find. I am in exchange with Karl-Heinz Rummenigge and Hasan Salihamidzic."
Bayern are third in the Bundesliga at the midway stage, four points adrift of leaders RB Leipzig after an indifferent first half to the campaign that saw Flick replace Niko Kovac in November.
Flick has overseen eight wins from 10 games in all competitions and will remain in charge of the German champions until the end of the campaign.
He previously worked as assistant to Germany coach Joachim Low for eight years before linking up with Kovac earlier this year, but that is no longer a role that appeals to him.
"I can imagine a lot of things, but I can't imagine that at the moment," he said.
"It's been a lot of fun, especially working with this coaching team and this squad.
"We've found a really good team spirit. Bayern Munich is a club with a lot of power, so I really like this job. The idea of always wanting to be successful suits me perfectly.
"I feel a lot of trust. There's nothing to stop us from continuing if we're successful. Let's just assume that our matches and results will remain satisfying. And if not, the club will have plenty of time to look for another coach."