Beard took Chelsea into their first FA Women's Cup Final this season, while also guiding the club through the inaugural FA Women's Super League campaign.
'After three years at the club, I have taken the decision to resign from my position,' said Beard.
'It has been an honour to work at this fantastic club. I am hugely proud of the progress we made, both on and off the pitch, which saw Chelsea Ladies secure their place in the new FA Women's Super League, as well as playing in this year's FA Cup Final.
'I would like to thank everyone at the club for their support over the last three years and I wish the club every success in the future.'
Chair of Chelsea Ladies Peter Steward said: 'Matt has decided to leave the club after three years and we'd like to thank him for all the hard work he's put in. He's done a fantastic job as manager of Chelsea Ladies and created a very strong squad.
'He felt it was the right time to move on ahead of the upcoming five-week break, which gives the club a chance to find a replacement.'
She Kicks - the online news service for women's football