US Vice President JD Vance lashed out at the EU amid rumours of its forthcoming fine on Thursday - claiming it was being punished "for not engaging in censorship".
"The EU should be supporting free speech, not attacking American companies over garbage," he said.
In addition to taking issue at its use of blue ticks, EU regulators said X was also failing to provide transparency around its adverts, and it was not giving researchers access to public data.
"The fine issued today was calculated taking into account the nature of these infringements, their gravity in terms of affected EU users, and their duration," the Commission said.
Henna Virkkunen, the regulator's executive vice-president for tech sovereignty, said it was "holding X responsible for undermining users' rights and evading accountability".
"Deceiving users with blue checkmarks, obscuring information on ads and shutting out researchers have no place online in the EU," she said.
The decision means X must tell the Commission how it will bring the allegedly violating measures into compliance with EU laws, or face further, periodic fines.
The action constitutes the Commission's first decision on a platform's "non-compliance" with its Digital Services Act (DSA) - one of two rulebooks online firms must follow in order to operate their services in the EU.
The DSA sets out obligations for platforms around content, data and advertising, while the Digital Markets Act establishes how companies should operate in order to benefit consumers and competition.
Such rules have come under increased scrutiny from US leaders, who warned against tougher regulation of tech firms by governments and regulators.