On the first count, the Commission said it had sent a formal "Statement of Objections" to Google, charging it with "systematically favouring its own comparison shopping product in its general search results pages."
"The Commission's preliminary view is that such conduct infringes EU anti-trust rules because it stifles competition and harms consumers," a statement said.
If found at fault under EU anti-trust rules, a company faces a fine of up to 10 percent of its annual sales -- in Google's case, USD 66 billion in 2014.
In a potentially hugely important development, it also announced a separate investigation into "Google's conduct as regards the mobile operating system Android."
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"The investigation will focus on whether Google has entered into anti-competitive agreements or abused a possible dominant position in the field of operating systems, applications and services for smart mobile devices," the statement said.
EU Competition Commissioner Margrethe Vestager said Android was hugely important and it was vital it be open to all.
Google accounts for about 90 per cent of the EU search market and now has 10 weeks to reply on the search count.
Vestager told a press conference that the door remained open to an amicable settlement and she called on Google to take every opportunity to discuss the issues with Brussels.
In two blog posts in response, Google said that in search, there was in fact "more choice than ever before."
The company said its Android system had been a key driver of innovation and had benefited others, not hindered them.
"We look forward to discussing these issues in more detail with the European Commission over the months ahead," the post said.