She is one of the few women to top the bill of any major festival, a sign of lingering male dominance of the music industry.
The festival's music is eclectic, with a huge rang of genres on offer including rock, indie, electronica and hip hop. The star's performance was dubbed "legendary".
Bey was originally slated to headline Coachella previous year but she dropped out on her doctor's advise after addressing her pregnancy with twins, Lady Gaga then took her place.
The superstar opened her set with hits like "Crazy in Love" and "Formation" before performing a remix of "Sorry", and she then belted out tracks including "Drunk In Love", "Diva", and "Flawless".More news: RNC official who agreed to pay Playboy model $1.6 million resigns
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Rousting said Beyoncé is a "perfectionist" who "has such a distinct vision for fashion and for her music".
"Thank you for allowing me to be the first black woman to headline Coachella", she exclaimed while bringing Sasha Fierce back to life.
Fans went wild as Beyonce and Destiny's Child went through hit after hit for almost two hours.
She stormed through almost every song she has ever released - including the world's quickest duet with husband Jay-Z - and even took the time to get a manicure halfway through the set. "So I had time to dream and dream and dream with two lovely souls in my belly, and I dreamed up this performance", she said. "I hope y'all enjoyed the show".