As of Tuesday, the popular discount site was listing tickets for weekday home games against the Indians and Mariners for $22, down from their $48 face value.
After 19 home games this season, the Yankees have an average attendance of 37,414 compared with 40,710 after the same number of games in 2012.
Groupon spokesman Tim DeClaire said the site has had a partnership with Major League Baseball since 2009 and has worked with 13 teams to sell tickets so far this year.
He added the Yankees didn't put up tickets on Groupon until June 13 last year.
The Yankees didn't return calls and emails seeking comment.
Steven Goldman, the manager of the Yankees blog Pinstripe Bible, said a lot of fans were put off by the injuries to all-stars like Jeter and Rodriguez, and because favorites like Nick Swisher were let go.
"They seemed to have missed the market," he said. "It became clear they were a team that was putting a product that wasn't worth the price."
Despite the depleted roster, the Yankees were tied for second place in the AL East going into last night's game. Attendance at Yankee Stadium has declined in the years since the team moved to its new home.
"Like many sports and entertainment entities, we use daily deal websites on a limited basis to promote special offers and one-off events to reach different audiences beyond sports," the Mets said in a statement.