Because multinationals in the EU pay their taxes in the country where they have their regional headquarters, countries have long competed among themselves to lure the companies.
That has resulted in countries offering tax advantages that allow the companies to pay very low tax overall and has become a big political issue as citizens in many European nations are forced to tighten their belt while some multinationals get away with huge tax breaks.
Today, it said that agreements Starbucks struck with the Netherlands and Fiat with Luxembourg years ago were not fair.
"All companies, big or small, multinational or not, should pay their fair share of tax," said EU antitrust Commissioner Margrethe Vestager as she announced the ruling today.
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She stressed the companies involved are not "the poster children of bad taxing behavior." Yet, she added that "these are examples of what is not right."
Starbucks said in an immediate reaction that it plans "to appeal since we followed the Dutch and OECD rules," referring to the Organisation for Economic Co-operation and Development, a watchdog for developed economies.
Both Luxembourg and the Netherlands also made clear they had objections to today's ruling and can appeal.
"The Netherlands is convinced that actual international standards are applied," the Dutch government said in a first reaction.
The government in Luxembourg said it "does not consider that Fiat Finance and Trade has been granted incompatible state aid."
The Netherlands must now recoup between 20 million and 30 million euros (USD 23 million and USD 34 million) from Starbucks and Luxembourg as much from Fiat. "This will remove the unfair advantage they have enjoyed," Vestager said.
She said the EU is investigating similar tax practices in all of the bloc's 28 nations.
"We do not stop here. We continue the enquiries into tax rulings," she said. "More cases may come if we have indications that EU state aid rules are not being complied with.