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.
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.
'Ask Me Anything'
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.
In December last year, the head of Heineken said that global beer consumption is holding up despite economic challenges, with employment strong and drinkers still treating higher-priced "premium" beer as an affordable luxury,
Chief Executive Dolf van den Brink told Reuters the Dutch brewer had seen signs of decelerating consumption in Europe, its largest market, in September after a very strong summer.
News by Reuters edited by Donna Ahern, Checkout. For more drinks stories click here. Click subscribe to sign up for the Checkout print edition.