Oscar Gutiérrez/CNET

Apple faces an investigation in Europe over Spotify's allegations of antitrust practices.

The European Commission, which handles the day-to-day business of the European Union, will launch a formal investigation in the coming weeks to probe Apple's practices with music subscription services, the Financial Times reported Sunday. Spotify filed an antitrust complaint in March.

In the complaint, Spotify said Apple charges subscription companies a 30% fee for in-app purchases while non-subscription apps don't have to pay any fee. Spotify stated in its complaint that Apple is attempting to stifle companies that compete with the Apple Music streaming service.

The iPhone maker responded in March saying the allegations were misleading and that "Spotify wouldn't be the business they are today without the App Store ecosystem." Apple also said the 30% fee drops to 15% after the first year and continues to drop the following years. Apple accused Spotify of wanting a "free ride."

Spotify revealed in its first-quarter earnings reports that it reached 100 million subscribers at the end of March and that 217 million people overall use its service at least once a month. In comparison, Apple said it had 50 million subscribers to Apple Music back in January.

Apple and Spotify didn't immediately respond to requests for comment.

Originally published May 6 at 6:46 a.m. PT.

Update, 7:09 a.m.: Adds latest subscriber numbers for Spotify and Apple Music.