The 21-year-old singer, who was nominated in six categories, became the most decorated artist in the history of the awards.
Bieber's first award of the night was Best Male, which he took home for the sixth year in a row. He beat out fellow stars Pharrell Williams, Kanye West, Jason Derulo and the awards show's host Ed Sheeran for the gong.
In his acceptance speech, he said, "Wow thank you it's been a long couple of years. I just feel like this is pretty awesome to be recognised for my music. I want to thank my fans, my mum my dad, God and everyone I love you thank you."
The singer also took to the stage for an incredible performance of "What Do You Mean?", cementing his triumphant musical comeback.
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His trophy haul gives him more MTV EMAs in his career than any other artist, however, Bieber did not manage to pick up his sixth award of the night, losing out to One Direction in the Best Pop category.
The boy band will go head-to-head with the pop star again on November 13, when both release their eagerly anticipated new albums on the same day.
Other winners on the night included Rihanna, who won Best Female and Nicki Minaj who picked up Best Hip Hop act. She was the only female act in the category and beat off strong competition from West, Kendrick Lamar, Wiz Khalifa and Drake.