The teen singer, who's been involved in a number of controversial incidents this year, was loudly booed when he accepted the Milestone Award (for "musical ingenuity and innovation," according to presenter CeeLo Green), the final award of the evening, beating out Bruno Mars and Taylor Swift. The award came after he had performed twice on the show.
"I'm 19 years old. I think I'm doing a pretty good job," a perplexed-looking Bieber said once the boos had died down. "It should really be about the music. It should be about the craft that I'm making. This is not a gimmick. I'm an artist and I should be taken seriously. All this other bull should not be spoken of."
The night's other big winners included Gotye and Rihanna, who each won four awards. Nicki Minaj won Best Rap Artist, and later gave Lil Wayne a lapdance during her performance. Madonna won three awards, including Top Dance Artist and Top Dance Album for MDNA.
And though she missed out on the Milestone Award, Swift won the most prizes of any artist, taking home eight trophies (of the 11 for which she was nominated), including Top Artist and Top Billboard 200 Album, for Red.
See a complete list of winners here, and watch video of Bieber's speech below: