Mendes had been expected to fare well, going into the EMAs with five nominations, and won for Best Artist, Best Fans and Best Song for "There's nothing holdin' me back". Singer Taylor Swift had more nominations, with six, but she didn't pick up any award.
The award ceremony was held inside London's SSE Arena, Wembley, on Sunday night, reports variety.com.
U2, recipients of the Global Icon Award on the night, performed "Get out of your own way" from Trafalgar Square.
Rapper Eminem was on the mic in a London pub before taking to the EMA stage and performed his new single, "Walk on water". The rapper picked up the Best Hip Hop gong.
Best Video went to rapper Kendrick Lamar for "Humble", Best Live Act to singer Ed Sheeran and Best Rock to Coldplay. Singer-songwriter Dua Lipa scooped the Best New Artist accolade.
Singer Rita Ora hosted and performed at the award ceremony, which was aired in India on Vh1. Mendes sung his Best Song-winning track "There's nothing holding me back".
Stars like Liam Payne, Travis Scott, Demi Lovato and Kesha also performed. French DJ David Guetta closed the show with his new single, "Dirty, sexy, money" with guests French Montana, Charli XCX and Afrojack.