Fox and Bay had an infamous falling out after the actress described the veteran producer as acting like Nazi dictator Adolf Hitler on the sets of 2007's "Transformers" and 2009's "Transformers: Revenge of the Fallen."
She didn't appear in the third installment, "Transformers: Dark of the Moon" in 2011.
However, Bay announced on his website Thursday he will be working with Fox again on "TMNT."
"We are bringing Megan Fox back into the family," Bay wrote.
No details about how the two buried the hatchet or what role the actress will play were immediately available.