The badges were worn by players last season following the global protests sparked by the death of George Floyd in the United States at the hands of a white police officer.
However, the Black Lives Matter group in Britain has been accused of anti-Semitism and criticised over calls to defund the police.
The league released a statement on June 30 saying it did “not endorse any political organisation or movement, nor support any group that calls for violence or condones illegal activity”.
Premier League captains were consulted over the change during a conference call on Thursday.
Instead of the BLM badge, the players’ shirts will have a new slogan reading “No Room For Racism” when the 2020/21 Premier League season starts on Saturday.
Premier League chief executive Richard Masters said: “We, our clubs, players and match officials have a long-standing commitment to tackling discrimination.
“Players rightly have a strong voice on this matter, which we saw last season. We have continued to talk and listen to players on this issue and will support them as well as continuing to emphasise the Premier League’s position against racism.”
The league said it would continue to support players who take the knee before matches in solidarity with the BLM movement.
