Giving her first public performance since announcing her pregnancy, the star took home best urban contemporary album for Lemonade and best music video for Formation.
On stage, she said the album was made to “give a voice to our pain” and to “confront issues that make us uncomfortable”.
The singer performed two songs from the hit visual album, as husband Jay Z and daughter Blue Ivy cheered from the audience.
Although Beyonce missed out in the main categories to Adele she did not leave empty handed.
During her acceptance speech after winning album of the year, Adele paid tribute to Beyonce, saying:
“I can’t possibly accept this award,” she said. “I’m very humble and I’m grateful and gracious but the artist of my life is Beyonce and the Lemonade album was just so monumental – Beyonce, it was so monumental.
“We got to see another side to you that we don’t always see. We appreciate that. All us artists here, we f****** adore you.”