The 19-year-old singer also bagged the awards for Best Song for his composition "There's Nothing Holding Me Back" and Biggest Fans, reported Variety.
In her acceptance speech, Mendes said, "Thank you to my fans. I love you guys. Also, the artists in this category are some people I've looked up to my entire life and to be nominated alongside them, it's crazy. Thank you for that. Thank you to my label, to my manager Andrew and my nan, who came with me tonight."
The show saw the comeback of rap god, Eminem, who performed his new single, "Walk on Water" and picked up the gong for Best Hip Hop track.
Music group U2 received the Global Icon Award and performed "Get Out of Your Own Way" from Trafalgar Square.
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Camila Cabello got the Best Pop award and also sang her song "Havana" and Dua Lipa took home the award for Best New Artiste.
The mention of Best Video went to Kendrick Lamar for "Humble", while Ed Sheeran and Coldplay bagged Best Live Play and Best Rock respectively.
The MTV EMAs aired on Vh1 in India.