"It's sad to see a print edition no longer exist, but it's important to see the Onion succeed," Mike McAvoy, president of Chicago-based Onion Inc., told Crain's Chicago Business.
The final print edition in the three markets will be Dec. 12.
The website, www.TheOnion.com, will remain in operation.
At its peak, The Onion's print edition was in 17 markets, but reduced advertising revenues forced the publication to cut back, BizTimes.com, Milwaukee, reported.
BizTimes.com said A.V. Club Milwaukee, which provided local content from The Onion's entertainment arm, The A.V. Club, also would shutter.
The Onion began in Madison, Wis., and expanded to Milwaukee.