It was the first time ever the veracity of the American leader’s claims were checked.
Twitter put a label under two of the president’s tweets, which claimed that mail-in voter ballots are subject to extreme fraud.
He stated that the ballots could be manipulated as some states are increasing access to postal voting to protect public health ahead of the November poll.
“Get the facts about mail-in ballots,” Twitter flagged and then redirects users to news articles and a bulleted list refuting Trump’s claims.
Reacting, Trump accused the company of “interfering” in the November presidential election and impinging on free speech.
“Twitter is completely stifling FREE SPEECH, and I, as President, will not allow it to happen!” he tweeted.
Twitter spokesman, Nick Pacilio, did not say whether or not the fact-check will continue but said the label is used “based on what people tweet”.
The platform has been under fire for allowing Trump, who has more than 80 million followers, “tweet anything at will”, according to critics.
His campaign manager, Brad Parscale, said: “Partnering with biased fake news ‘fact checkers’ is a smoke screen to lend Twitter’s obvious political tactics false credibility.
“There are many reasons we pulled all our advertising from Twitter months ago, and clear political bias is one of them”.
Last year June, Twitter announced that it would mark tweets that violate its policies on such things as abusive behaviour and public safety.