The British actress, 33, was fresh out of drama school before filming her first scenes as exiled queen Daenerys Targaryen in 2010, taking on a role she held until this year's eighth and final season.
Speaking with Dax Shepard on his "Armchair Expert" podcast, the star reveals she was uncomfortable with what was asked of her during filming on the early seasons - and had to push back to cut her nude scenes as the show progressed.
"I'm a lot more savvy (now) with what I'm comfortable with, and what I am OK with doing. I've had fights on set before where I'm like, 'No, the sheet stays up', and they're like, 'You don't wanna disappoint your Game of Thrones fans.' And I'm like, 'F**k you,' " she explains.
She admits she found the amount of nudity in season one "overwhelming" and her lack of experience made sex scenes awkward, even when she was happy that they were essential to the script.
Emilia adds, "I've never been on a film set like this before, I'd been on a film set twice before then, and I'm now on a film set completely naked with all of these people, and I don't know what I'm meant to do and I don't know what's expected of me, and I don't know what you want and I don't know what I want."
However, the star praised Jason Momoa, who played her onscreen husband Khal Drogo, for interceding with directors and crew and ensuring she did not have to do anything that made her feel uncomfortable.
"It was definitely hard. Which is why the scenes, when I got to do them with Jason, were wonderful, because he was like, 'No, sweetie, this isn't OK.' And I was like, 'Ohhhh,' " the actress reveals.