The British news agency Reuters reported that the Cupertino-based firm could face a fine amounting to as much as 10% of its global revenue.
The EU has been unable to sting Apple in the past, with the company defeating a bid by the political bloc to make it pay €13 billion (A$21 billion) in back taxes.
Four years after the EU made the demand, Apple prevailed in the Luxembourg General Court, which said "the Commission was wrong to declare" that Apple "had been granted a selective economic advantage and, by extension, state aid".
Apple was hit with the fine in August 2016, after the EU said it had found the company had cut a number of illegal deals in Ireland in order to do business.
The EU has appealed against the verdict and is taking it to the European Court of Justice.
Spotify, a Swedish company, approached the European Commission in 2019, and also complained about the 30% commission that Apple charges app developers.