McCoy is pregnant and so is currently unable to reprise her role of Milady on the BBC drama, reported Digital Spy.
However, a BBC spokesperson has confirmed that the actress is in talks to return to the show at a later date.
"We are delighted for Maimie and wish her well through her pregnancy. We very much hope she may come back as Milady in the latter half of series 3 and are in discussions with her to that effect."
It is currently unclear how many episodes McCoy will miss as a result of her pregnancy.
The pair will appear alongside returning cast members Luke Pasqualino, Tom Burke, Howard Charles, Santiago Cabrera, Hugo Speer, Ryan Gage, Alexandra Dowling and Tamla Kari.
New episodes have been shooting in Prague since April.