During the episode, drag queen Jackie Cox, real name Darius Rose, wore a star-spangled hijab in honour of her Muslim background, as part of the show's Stars And Stripes runway challenge.
Commenting on the look, Jeff, 67, came under fire by first asking if the performer was "religious" before going on to question the treatment of LGBTQ+ people within the faith.
"Is there something in this religion that is anti-homosexuality and anti-woman? Does that complicate the issue? I'm just raising it and thinking out loud and maybe being stupid," he commented.
While RuPaul insisted that "drag has always shaken the tree," Jackie became teary-eyed as she said it was "a complex issue" and she had her "own misgivings about the way LGBTQ+ people are treated in the Middle East."
"I had to show America that you can be LGBT and from the Middle East and there's going to be complicated s**t around that and that's okay. But I'm here and I deserve to be in America just as much as anyone else," Jackie said.
Criticising the "Jurassic Park" star for his theories, fans took to Twitter to make their feelings known, with one viewer writing, "That Jeff Goldblum to Jackie Cox moment on this week's Drag Race was so deeply uncomfortable to watch."
"Why did he think that was appropriate? How did it make it to the edit? How was that in any way fair on Jackie? Just so many levels of awfulness."
Another commented, "Now would Jeff Goldblum have asked a Christian queen that same question that he asked Jackie? That was really ignorant," while a third user hit out, adding, "I am REALLY not here for Jeff Goldblum's casually islamophobic critique of Jackie Cox tonight."
The star has yet to comment on the controversy.