"That would destroy the security of the iPhone and a lot of the privacy initiatives that we've built into the App Store where we have privacy nutrition labels and app tracking transparency, where it forces people to get permission to track across apps," Cook said.
"These things would would not exist anymore except in people that stuck in our ecosystem and so I worry deeply about privacy and security."
The Apple CEO said Android has 47 times more malware than iOS, and this was directly due to Apple's ecosystem being tied down to one app store and all apps being reviewed.
"That keeps a lot of this malware stuff out of our ecosystem, and customers have told us very continuously how much they value that, and so we're going to be standing up for the user in in the discussions and we'll see where it goes," he said.
Cook did say there were parts of the Digital Services Act (DSA) that could be used to fight online disinformation.
"We do suffer today from vast disinformation ... it's clear that there needs to be something done here," he said.
"This is not an acceptable state of the world and as I look at the DSA, there's some parts of it that I think will help this, but I'm not sure that anybody yet has a handle on how to fix it entirely and I think it deserves more discussion and more debate."
In recent testimony as part of the Epic vs Apple trial, Cook said without curation, Apple's App Store would be a toxic mess.