As the goalie's contract with the Royal Blues is running out next summer, he signed a five-year contract with the ruling German champion until 2025.
But looking at the circumstances after the deal was officially announced on Saturday morning, things seem much more enigmatic, Xinhua news agency reported.
The deal isn't only causing turmoil for Nuebel at his current club over the upcoming months as the country's most talented keeper might lose his place in the starting eleven, his captain's band and find himself sitting on the bench until the end of the season.
Thousands of Schalke fans have demanded to remove their former hero from the squad and want to see his "treasonable act" rewarded with a regular place on the main stand.
Bayern's undisputed number one, Manuel Neuer, is reported to oppose the plans of Bayern sports-director Hasan Salihamidzic to share the goalkeeping job.
According to media reports, Salihamidzic demanded from the 33-year-old German international to make space in 15 season games. Neuer refused to accept the offer, several media reports said.
While the club's coaching issue remains unsolved as Hansi Flick is only in charge until the end of the 2019-20 season, a new delicate case is now waiting to be decided.
On top, Bayern intends to extend Neuer's contract until 2023. The deal is in danger, some pundits assumed.
( With inputs from IANS )