The Open Internet Project, which made the complaint, accused Google of "contractual restraints on manufacturers of Android smartphones and tablets, which make it virtually impossible for them to produce and market Google-free devices".
This is the third complaint lodged with the EU against Google.
Last April, the EU issued a chargesheet to Google, accusing the search giant of breaching EU anti-trust rules.
Google also faces EU charges that it has abused its search monopoly for which it may be fined up to €6.6 billion, a tenth of its annual sales.
The company could suffer in terms of business as well. According to the EU, Google Play, the Android app store, accounted for 90% of all apps downloaded in 2015.
Wednesday's complaint by the OIP claims Google is giving prime position to its own search engine in its Chrome browser, and others, such as Qwant (which is a French product), are not offered as a choice to users.
Google has avoided being hauled over the coals in the US because it wielded considerable political clout during the last Democrat administration, with its officials having access to the White House regularly.
The company has also gained a foot in the Trump regime, with a former executive, Joshua Wright, being put in charge of transition efforts at the Federal Trade Commission.