It might well still be the biggest in the EU if you drew limits based on what people considered part of the city - I don't know - but it certainly would not be as big as its urban area.
In fact, I'd argue you're unlikely to find any major city anywhere in the world where most people would agree that every part of the outer boundaries of the urban area are part of "the city" (or even "a city"; parts of urban areas will still often be considered fairly rural by those who live there or in the nearby city) even in a loose colloquial or cultural sense. Even coming close would be exceedingly rare. This because the ways urban areas are designated by design tends to include commuter regions far outside, with their own identities, and often very separated from the biggest city in the urban area.
So while going by city limits will be misleading, so will going by urban area. Unfortunately, no single metric will be accurate for these things.
I live outside of London, howver you define 'London', but still in London's area of influence considering how many people commute into London from here every day.
At the same time it's specifically meant to be aligned to OECD and Eurostats definition of a Functional Urban Area, which is a definition meant to ensure comparable statistics across countries, which neither the "old style" urban nor metropolitan area terms provide...
Which really just goes back to the main point that you can get pretty much whichever result you want here unless you narrow it down to the specific criteria that actually matter to you...
Paris has the specificity of having small limits for the city proper but it does not make sense to use that metric for comparison because nowadays the city only stops at the administrative limits for adminsitrative purposes and nothing else. You won't even notice you've crossed the limit if not for the ring road.
In fact, Moscow is also larger than Berlin however you look at it we we're talking about "continental Europe" (which I take as a way to exclude London, which is also larger than Berlin...).