The Commission's Apple fine was delivered in April alongside a penalty on Facebook owner Meta of €200m (£171m) over choice for users under its "consent or pay" model.
The fines were the first imposed under the EU's Digital Markets Act (DMA) - its landmark legislation designed to boost competitive business practice in online markets.
The law also carries tougher obligations for companies designated dominant "gatekeepers" in certain sectors, and firms face hefty fines of up to 10% of their annual global turnover for rule breaches.
Henna Virkkunen, the Commission's executive vice-president for tech sovereignty, security and democracy, said at the time that both companies had undermined the key principles of the DMA - to enable free business and choice for consumers.
Apple said it was being "unfairly targeted" and forced to "give away our technology for free".
It also accused the regulator of "[moving] the goal posts" during their meetings.
It has now escalated its complaint to the EU's second highest court, the General Court.
The EU's strict regulation of large US tech firms has also attracted scrutiny from President Donald Trump's administration.
Trump said in January that he had "some very big complaints with the EU" regarding its treatment of American tech companies, likening fines upon them to "a form of taxation".
Speaking on a podcast in October, he said Apple's boss Tim Cook had also called him to complain about the bloc's fines.