The actress - who plays the female version of The Master, Missy - will bow out from her role at the end of the current series, just as showrunner Steven Moffat also departs.
Speaking to Digital Spy, Michelle said: “My guys, my lads, Missy’s men - they’re all moving on!
“I’m probably just shooting myself in the foot here. This time next year, I’ll be like, ‘Why did I say that?! I’ll work for anybody!’ – but I don’t know how I’d feel about being The Master to any other Doctor, because I feel like I’m part of Peter’s time.”
However, she has not ruled out a return later down the track, adding: “I’m sure in a couple of years’ time, the urge to blow things up will just be too strong and Missy will come in guns blazing!
It was previously revealed John Simm will be reprising his role as the previous incarnation of The Master later in the series, and it is thought he will appear alongside Missy.
Meanwhile, it looks as though new assistant Bill, played by Pearl Mackie, could also be leaving, despite only joining at the start of the series, giving new show boss Chris Chibnall a clean break from the current cast.
Many names have been linked to succeeding Peter Capaldi as The Doctor, including Kris Marshall and Ben Whishaw.
‘Fleabag’ star Phoebe Waller-Bridge also recently spoke out about the rumours she was set to become the first female star to take on the character.
‘Doctor Who’ continues at Saturday (20 May) at 7.25pm on BBC One.