After taking over from Niko Kovac in November 2019, the 56-year-old led the Bavarian side to a Bundesliga, DFB-Pokal and UEFA Champions League treble in his first campaign in charge.
He added a UEFA Super Cup, DFL-Supercup and the FIFA Club World Cup this term, with another top-flight title also looking likely after Bayern opened up a seven-point lead on Sunday (AEST) with a victory over Wolfsburg.
However, it has recently been reported that Flick was considering his future and, speaking after the 3-2 win over Wolfsburg, the German coach revealed he will depart at the end of the season.
That means one of the biggest jobs in European football is about to become available – so who is in the running to step into the role?
One of the most well-regarded young coaches in Europe, Julian Nagelsmann has long been admired by the decision-makers at Bayern Munich.
With speculation mounting over Flick earlier this week, the 33-year-old was forced to deny that discussions with Bayern had already begun.
"There have been no talks and we are currently in no talks," he said.
It has been previously reported that RB Leipzig would demand up to €20 million ($31.2 million) to release its head coach from his contract.
But Bayern could well view that as a snip for a manager who has long been touted for the top job in German football and has previously attracted interest from Real Madrid.
The last manager to deny Bayern the Bundesliga title, Jurgen Klopp is another man who Die Roten have made no secret of their desire to appoint one day.
Despite his ties with Borussia Dortmund, the 53-year-old has never publicly declared that he would not make the move to Munich at some point in his career.
He has, however, recently signalled his intention to see out the remainder of his contract at Liverpool.
Amid links to the soon-to-be-vacant Germany job, Klopp said: "You sign a contract and you normally try to stick to that contract, don't you?"
Schalke, Eintracht Frankfurt, Germany – nobody seems to know where Ralf Rangnick might go next.
Out of work since leaving a role with RB Leipzig in 2019, the 62-year-old's appointment would not require any costly negotiations with a rival.
While he might represent a slightly left-field choice to be the new Bayern boss, nobody can doubt his coaching credentials.
So many of the managers the Munich club covet have been influenced by Rangnick, so why not go for the original?
Flick's imminent availability comes amid strong links with the role of head coach for the German national team.
That vacancy has come up as a result of Joachim Low revealing that he will bring a 15-year stint in the job to a close after the European championships.
So, could the 61-year-old take on his first job in club management since he took charge of Austria Wien for the 2003-2004 season?
Low's only trophy in German football came when he led Stuttgart to the DFB-Pokal in 1997, but his resume is certainly enhanced by that FIFA World Cup win in 2014.
Having enjoyed remarkable success since Flick stepped up from his role as assistant to Kovac, Bayern could choose to go down a similar route after his departure by appointing Miroslav Klose.
The Germany legend moved up from his role as under-17s coach over the summer to become second in command for the first team and might be a surprise choice for another promotion at the end of the season.
The 42-year-old is popular with supporters, but his lack of experience might count against him given the quality of the other candidates.
Still, if Bayern values continuity above all else in its search for a Flick replacement, don't count Klose out.