The letter said a small number of employees will remain working in the warehouse at the 1843 S. Washtenaw Ave. location.
The closure is expected Aug. 1, the letter said.
In a news release, the brewery said it plans to move its Chicago brewing operations to Lagunitas' original brew house in Petaluma, California.
The changes will affect 86 employees, some of whom will retain remote roles or relocate to California, the release said.
Others will receive retention incentives to work through the transition, as well as departure packages, including support services and job-placement assistance, the release said.
"We are committed to managing this transition thoughtfully, smoothly and with deep respect for our valued Chicago Lagunitas employees," said Sam Kennedy, a Lagunitas spokesperson.
The release said the changes were prompted by a need to future-proof the organization amid changing tides in the craft beverage industry.
"The transition will allow for a more efficient and flexible supply chain, with a greater focus on innovation and the acceleration of more sustainable brewing practices. Chicago remains a priority market for Lagunitas, and the company will continue servicing the many partner bars, restaurants, and stores in and around Chicagoland with its fresh and high-quality hop-forward IPAs and other brews," according to the news release.
In 2017, Heineken bought the craft beer-maker.
Heineken helped the craft brewer enter markets in Europe and Mexico. Lagunitas is now available in more than 50 countries.
Lagunitas has headquarters in Chicago's Douglass Park neighborhood and Petaluma, California.
The Chicago brewery opened in 2014.
It closed to visitors for an extended amount of time during the COVID pandemic, but had somewhat recently reopened.
"There's no way to sugarcoat this news, but it's a decision that is right for us in the long run. Right now, it sucks," Lagunitas said on its website. "Cheers to the nights spent pouring beers, dancing to killer live music, and sharing countless unforgettable memories."
Lagunitas founder Tony Magee was a native Chicagoan, graduating from Buffalo Grove High School. He started making beer in 1993 with a home brew kit in Northern California and by 1995, he developed India Pale Ale, according to the company's website.
He launched Lagunitas in Chicago in 2014 with help from Nick Mirkopolous, owner of film studio Cinespace.
The Chicago brewhouse could produce more than 500,000 barrels of beer per year and had capacity to brew and ship 1 million barrels a year, making it larger than all the other craft breweries in Chicago combined in 2014.
"It's unfortunate, but I don't think the space will stay empty for long," said 24th Ward Ald. Monique Scott, who represents the neighborhood where Lagunitas is located. "I'm very optimistic because it's a great space."
She mentioned the possibility that another brewery could open at the site.
Scott said after Heineken bought Lagunitas, the craft brewer was "not as community-focused as when they opened. It kind of changed the brand."
Sun-Times Media contributed to this report.