Mr Biden's team "fought" the plan, but the social media giant said its decision was "unequivocal". The move marks a reversal from the last transition.
Twitter agreed to Donald Trump's request in 2016 to inherit Barack Obama's millions of followers.
“In 2016, the Trump administration absorbed all of President Obama's Twitter followers on @POTUS and @WhiteHouse - at Team 44's urging,” Rob Flaherty, the president-elect's digital director, tweeted on Monday. “In 2020, Twitter has informed us that as of right now the Biden administration will have to start from zero.”
It affects followers of government-led accounts such as @POTUS and @FLOTUS, all of which will be transferred to Mr Biden when he takes over the presidency in January. Twitter said those who follow the current presidential accounts will be notified that they are being archived, and will be given the choice to follow the Biden administration's new accounts. Mr Biden’s personal account, @JoeBiden, has 21.7 million followers, and will be unaffected by the move.
President Trump has famously used his Twitter accounts, both professional and personal, to engage with voters. During his time in the White House, he has tweeted more than 50,000 times.
However, according to Factbase, a website that tracks tweets and follower counts, Mr Trump has lost 369,849 followers on his personal account since November. In the same timeframe, President-elect Joe Biden has gained 2,671,790 followers.
The decision from Twitter comes just days after chief executive Jack Dorsey unfollowed numerous political figures on the platform, including Mr Trump, Mr Biden and Vice-President-elect Kamala Harris.
Marketing specialist Rebecca Lodge, from Start Up Disruptors, said of Twitter's decision: "With millions of people following an account and Donald's 'fans' being quite fanatical, it could be a clever move by Twitter to ensure that any potential negative and hate-fuelled tweets are neutralised before the new president-elect takes up his position."