Earlier this month, the European Union unveiled a list of the digital giants, including Apple, which will face new rules under the Digital Markets Act (DMA) on how they do business.
Other tech firms caught up included Facebook owner Meta and TikTok parent ByteDance.
Apple has previously slammed the DMA, claiming it poses risks to users' privacy.
Cook was in Brussels to meet with Breton and the acting competition commissioner, Didier Reynders.
"The next job for Apple and other big tech, under the DMA, is to open up its gates to competitors," Breton said, in a statement.
"Be it the electronic wallet, browsers or app stores, consumers using an Apple iPhone should be able to benefit from competitive services by a range of providers," he added.
Breton said the two men had a "constructive discussion on Apple's compliance plan" for the DMA.
Apple would not comment on Cook's visit.
The EU however won a previous battle with Apple, forcing the company to unveil its new iPhone lineup with a universal charger on September 12.
Brussels' rules insist all phones and other small devices must be compatible with the USB-C charging cables from the end of next year.
Breton showed Cook his "museum" with several charging cables in a video shared on social media after hailing "cable clutter" as "a thing of the past" in his statement.
The latest battle began when the EU on September 6 named Apple's operating iOS system, its App Store and its Safari browser as services that must comply with the DMA.
Brussels is also probing whether to include iMessage in that list.
Shortly after the announcement, Apple said it was "very concerned about the privacy and data security risks the DMA poses for our users" and vowed to focus on "how we mitigate these impacts".
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