The filing by the Netherlands' Financial Markets Authority (AFM) said the shares were purchased on 17 February. Heineken Holding owns a controlling stake in brewer Heineken NV.
Gates purchased the shares from Mexico's FEMSA, which is selling out of the brewing company.
A separate filing also dated 17 February showed FEMSA sold all 18 million shares it held in Heineken Holding. Gates purchased 10.8 million shares, worth €883 million ($939.87 million) at current market prices, triggering a disclosure requirement under Dutch stock market rules.
'Not A Big Beer Drinker': Gates
In a 2018 'Ask Me Anything' chat session on Reddit, Gates said he was "not a big beer drinker."
"When I end up at something like a baseball game I drink light beer to get with the vibe of all the other beer drinkers. Sorry to disappoint real beer drinkers."
The Bill & Melinda Gates Foundation, the charitable foundation launched by the billionaire and his former wife, wasn't immediately available for comment.
Meanwhile, Heineken said it still plans to exit Russia and sell its business there at a loss this year, after a Dutch media report questioned whether it had followed through on its March 2022 promise to leave the country.