Mondelez is one of the largest chocolate, biscuit and coffee producers in the EU, the Commission said.
Mondelez, which owns brands including Toblerone and Milka, said it will "work constructively" with the Commission.
In the EU single market, retailers and traders try to buy products where they are cheaper and trade them in countries where the prices are higher.
This tends to push the prices down in the more expensive countries.
However, the formal investigation will look at whether the US snack giant limited where traders could buy and sell products to particular sales territories.
The Commission will also look into whether Mondelez raised prices or limited volumes for firms that traded across the EU.
It will probe whether Mondelez paid or compensated firms so they wouldn't make that kind of cross-border trade, and whether it refused to supply certain traders to restrict imports.
Executive Vice-President Margrethe Vestager, in charge of competition policy, said: "Chocolates, biscuits and coffee are products consumed by European citizens daily.
"We are opening a formal investigation to see whether Mondelez, a key producer of these products, might have restricted free competition in the markets concerned by implementing various practices hindering trade flows, ultimately leading to higher prices for consumers."
Mondelez said: "We will work constructively with the European Commission as it conducts its review."
Commission investigators made a series of raids on Mondelez premises in November 2019 after concerns were raised that prices for food and drinks products significantly varied across EU member states.
In May 2019 the Commission fined beer giant Anheuser-Busch InBev €200m (£176m) for using similar methods to ensure that cheaper beer from the Netherlands and France could not be sold in Belgium.
This included changing the design and size of beer cans to make them unavailable for cross-border sales.
In 2019, Mondelez sales reached $25.9bn (£19bn) worldwide and the company is due to report financial results for 2020 later on Thursday.