The superstar led all nominees heading into the show with 11 nods for her groundbreaking Lemonade album and short film, and she quickly racked up the prizes, earning Best Choreography, Best Direction, Best Cinematography, and Best Editing for Formation, which she performed as part of a show-stopping Lemonade medley.
Formation also earned Beyonce the coveted Video of the Year title, which she dedicated to the residents of New Orleans, Louisiana, who have been struggling with severe flooding in recent weeks.
Read more: Beyoncé cleans up at the BET Awards
With her multiple victories, she broke the record for most VMAs with 21 wins, surpassing the previous title holder Madonna, who has a total of 20 Moonman trophies.
Rihanna was another big winner at the VMAs, which she opened with the first of four performances during the New York show, singing hits Only Girl (In The World), We Found Love, and Where Have You Been.
She later returned to the Madison Square Garden stage to belt out tracks like Work, Needed Me, Stay, and Diamonds before she was presented with the prestigious Michael Jackson Video Vanguard Award by her frequent collaborator and rumoured boyfriend Drake.
He delivered a heart-warming speech hailing the R&B beauty's achievements, declaring he had been "in love" with her since he was 22, and honouring Rihanna as a "living, breathing legend in our industry".
They then shared a kiss on the cheek as Rihanna stepped up to accept the special Moonman award, which she celebrated as "such an amazing moment" in her career.
The Bajan star then went on to thank her longtime fans, saying: "My success, it started as my dream, but now my success is not my own; it's my family's, it's my fans, it's my country's, it's the Caribbean as a whole, it's women, it's black women... So many people feel like their little piece is such a major part of this puzzle and I have to thank you guys for supporting me, over and over..."
The Video Vanguard Award wasn't her only win of the night - she also helped Calvin Harris claim the Best Male Video title for their latest collaboration, This Is What You Came For.
Other performance highlights came from Ariana Grande and Nicki Minaj, Britney Spears and rapper G-Eazy, and Nick Jonas, who took over Manhattan's Tick Tock Diner for a rendition of Bacon with Ty Dolla $ign.
The main winners from the 2016 MTV Video Music Awards are:
Video of the Year: Beyonce - Formation
Best Male Video: Calvin Harris featuring Rihanna - This Is What You Came For
Best Female Video: Beyonce - Hold Up
Best Collaboration: Fifth Harmony featuring Ty Dolla $ign - Work From Home
Best Hip-Hop Video: Drake - Hotline Bling
Breakthrough Long Form Video: Beyonce - Lemonade
Best New Artist: DNCE
Song of Summer: Fifth Harmony featuring Fetty Wap - All In My Head (Flex)
Best Art Direction: David Bowie - Blackstar
Best Choreography: Beyonce - Formation
Best Direction: Beyonce - Formation
Best Cinematography: Beyonce - Formation
Best Editing: Beyonce - Formation
Best Visual Effects: Coldplay - Up&Up.
© Cover Media