The Senegal international joined the German giants on a season-long loan for a 14m-pound fee, with a further 56 million due had certain appearance criteria been met.
The clause required Jackson to make 40 appearances of at least 45 minutes each. However, he has featured 22 times in total and reached the 45-minute threshold in only seven matches, leaving the trigger well short.
Jackson has struggled to cement a regular place in Vincent Kompany's starting XI, scoring five goals across all competitions.
Despite those challenges, Kompany has spoken positively about the forward's application and impact within the squad. Nevertheless, Bayern have no plans to negotiate a separate permanent transfer.
"He's helped us a lot. Of course, with Harry Kane up front, you have a bit of competition, and that's part of the game," Kompany said back in December.
"So, as a coach, it's a real luxury to see how Nicolas is handling that. What many people don't see is what Nicolas does in training and every time he comes on. Hopefully, he'll continue to capitalise on the chances he gets."
His campaign was also interrupted by international duty, as he represented Senegal at the Africa Cup of Nations, playing five matches during their title-winning run.
Back at Stamford Bridge, new head coach Liam Rosenior will assess Jackson during pre-season.