The group received a surprisingly negative reaction when they collected the gong for 'Song of the Summer' - for their hit single 'Best Song Ever' - and while they took it in their stride, they still had the support of the 'Applause' singer.
Seen backstage after the boy band accepted their award, Gaga was heard saying: "Don't you dare let those people boo you. If I did hear what I heard out there, I just want to tell you that you deserve every bit of success that you have.
"I want to leave right now. I don't want to stay anymore because I don't want to be in a room where people are booing."
Liam Payne took to his Twitter account earlier on Monday and thanked the star for her kind words.
He wrote: "Morning everyone what a night yesterday was would like to thank @ladygaga for her support yesterday and her extraordinary outfits."
Earlier in the night, Taylor Swift was seemingly caught on camera turning to Selena Gomez and telling ex-boyfriend Harry Styles to "shut the f**k up" while his was on stage with his band mates to present the award for Best Pop Video.