Apple CEO Tim Cook attends the annual session of China Development Forum (CDF) 2018 at the Diaoyutai State Guesthouse in Beijing, China March 26, 2018.

Spotify's App Store complaint — filed with the European Commission's antitrust regulators and revealed Wednesday — carries "meaningful risk" for Apple and its burgeoning services revenue, analysts for KeyBanc said in a note Wednesday.

The complaint takes issue with Apple's control of its App Store, claiming the company deprives consumers of choice and imposes unfair restrictions and fees on competitors. Apple takes a 30 percent cut of most in-app purchases made through the App Store, which disproportionately affects subscription companies like Spotify.

"We believe Spotify is largely on the right side in both facts and principle, which creates risk that App Store policy terms will be forcibly changed in a way that negatively impacts Services revenue and Apple's brand," analysts at KeyBanc wrote in the note.

Apple prevents companies from linking to alternative payment methods that would circumvent the 30-percent cut, which KeyBanc says "holds no practical purpose other than to force competitive services into higher cost structures and unfairly tax service activity on the iOS platform."

App Store revenue continues to rise, as more subscription companies launch on the service. KeyBanc estimates App Store revenue will total $13.4 billion and account for 12 percent of Apple's gross profit for the fiscal year 2019.

Apple's Chief Financial Officer Luca Maestri attributed part of that growth to third-party app subscribers during the company's most recent earnings call, but downplayed the importance of any one subscriber.

"Our subscription business has become very large and diversified, covering many different categories, from entertainment to health and fitness to lifestyle," Maestri said. "More than 30,000 third-party subscription apps are available today on the App Store, and the largest of them accounts for only 0.3 percent of our total Services revenue."

The situation could get more complicated as Apple plans to release more of its own first-party streaming services. The company is expected to announce new video and news subscription services at an event at its headquarters on March 25.

Apple has not yet issued a response to Spotify's complaint.

—CNBC's Elizabeth Schulze contributed to this report.

WATCH: Spotify files an EU antitrust complaint against Apple