The days of Silicon Valley's favorable tax treatment in Europe may be over, as the European Union moves to crack down on what it has deems an epidemic of unfair deals in the region. Inc. (AMZN - Get Report) and Apple Inc. (AAPL - Get Report) are the latest U.S. tech giants to land in the crosshairs of the European Commission, the EU's antitrust watchdog. On Wednesday, the EU ordered Amazon to repay $293 million in back taxes to Luxembourg, where its European headquarters is based, after the EU deemed that Amazon was receiving illegal tax benefits.

That's after the EU announced separately that it would take Ireland to court over failing to collect as much as $15 billion in taxes from Apple. The Commission began investigating Ireland's favorable tax deal with Apple in 2014 and concluded in 2016 that Apple was breaking state aid laws. Ireland, which called the lawsuit "wholly unnecessary," has failed to meet the deadline for collecting the repayment from Apple. 

The moves mark the latest chapter in the EU's growing offensive against U.S. tech companies, one which has partly unfolded this summer and has included investigations into Facebook Inc.  (FB - Get Report) , Alphabet Inc.  (GOOGL - Get Report)  and Qualcomm Inc.  (QCOM - Get Report) . Margrethe Vestager, the EU's competition commissioner, has been a vocal force in the EU's battle against Silicon Valley. 

European Commissioner for Competition Margrethe Vestager
European Commissioner for Competition Margrethe Vestager

Germany and France have been the clearest supporters of the EU's plan to collect more taxes in the region, arguing that tech giants have been skirting regulators by basing their European headquarters in lower-tax EU states such as Ireland and Luxembourg. Proponents of the EU's increased oversight argue that recent EU-wide tax increases ended up impacting small businesses the most, as large tech companies were able to avoid them by moving profits to low-tax regions. A recent study from the UK-based Centre for Economics and Business Research found that the U.K.'s bookshops pay 11 times what Amazon does in corporate tax, according to the Guardian.

Amazon said in a statement on Wednesday that it would consider appealing the EU's decision. Apple has already set it will appeal the case. 

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The EU has proposed reforms such as taxing revenue instead of profits, as is currently the case, to make sure it gets its fair share of tax revenue from U.S. tech companies, said Jan Dawson, chief analyst at Jackdaw Research. EU finance chief Pierre Moscovici has said the proposal boils down to fairness, in that many tech companies rely on European networks and infrastructure, so they should be taxed the full and fair amount. 

The EU is expected to weigh the proposal to tax revenues on Wednesday as part of a broader discussion of sales tax reform. Some of the sales tax regulations have already been implemented on a temporary basis, but those changes could be made permanent. 

Without the full support of all members, it's unclear whether those resolutions would ever pass. Ireland, for example, would rather keep the tax environment friendly in order to continue attracting U.S. tech giants -- and their jobs -- to the region. Danish Finance Minister Kristian Jensen recently remarked that he was "skeptical" about new taxes and was concerned that such a move would drive digital industry elsewhere.

The American Chamber of Commerce in Europe has also pushed back on the EU's efforts, saying they could "harm the competitiveness of the EU" and dissolve further conversations between the EU and the US on global tax reform. 

Ultimately, the regulations are unlikely to impact tech giants' business overseas, however. 

"It's not a threat to these companies' overseas operations, but it will see them pay higher tax rates than in the U.S. on that revenue if it's taxed there," Dawson explained. 

In addition, there are other ongoing efforts by the EU that might pose a greater threat to Silicon Valley than higher taxes. The EU is set to pass a set of new, stricter privacy rules by May 2018, known as the General Data Protection Regulation (GDPR), that would allow the EU to fine tech companies up to 4% of their annual revenue for privacy violations. Under the new laws, users can opt out of giving personal data. The GDPR rules could represent a gigantic shift in how some companies, especially Facebook and Google, typically collect data, since people don't usually pay much attention to a website's terms and conditions. 

"Significant fines may cause industry participants, including marketers (who could be liable for fines themselves), to become hyper-cautious in use of media owners' data, and invest more heavily in first-party data," said Pivotal Research analyst Brian Wieser in a recent note. "This could limit the advantages that Google and Facebook possess."