The lyrics "don't be a drag, just be a queen", which are used to bridge between the first chorus and second verse, were replaced by a dance performance.
The entire third verse was also removed, cutting out the song's most iconic lyrics which call for equality.
Fans were quick to take to social media to slam the show and the BBC for the decision, with some even suggesting the judges should be made to resign.
The BBC has not yet commented on why those lyrics were cut.
Iron Sun was eliminated from the competition after receiving the least votes from the public.
The performance comes just a few weeks after Lady Gaga sang the song at the Superbowl, where she was praised for singing the pro-LGBT lyrics to an audience of football fans.
Let it Shine airs in New Zealand on UKTV.