The actor refuses to go into great detail about the much-rumoured romance and has no idea if Fox was dating Brian Austin Green, who is now her husband, at the time - but he has revealed that something was going on behind the scenes on the first two action blockbusters.
LaBeouf tells the new issue of Details magazine, "You're on the set for six months, with someone who's rooting to be attracted to you, and you're rooting to be attracted to them.
"I never understood the separation of work and life in that situation. But the time I spent with Megan was our own thing, and I think you can see the chemistry onscreen... It was what it was."
Green and Fox briefly split during the making of the Transformers movies but they reconciled and wed last year (Jun10) in Hawaii.
The couple renewed their vows on their one-year anniversary recently.
Fox has since been replaced by model/actress Rosie Huntington-Whitely as LaBeouf's love interest in the latest Transformers film, Dark of The Moon.
In the Details interview, LaBeouf also opens up about romances with actresses Carey Mulligan and Isabel Lucas, who also starred alongside the actor in the Transformers sequel.
Of his time with Lucas, the star says, "It was sort of disastrous... Neither one of us, I think, were in love. Just sort of experimenting or whatever."
But it's clear British actress Mulligan, who he romanced through 2010, meant an awful lot to him."
He explains, "I still love her... I think she's a f**king awesome person and an incredible actress. We're still pals. I wouldn't take any of it back, and I don't think she would either. It just ran its course."