The late-night show, which followed Conan, averaged 500,000 viewers, losing more than 350,000 viewers from its lead-in. The series will go off the air on June 19.
"We recognize Pete as one of the most relevant comedians working today," TBS said in a statement. "We loved the show and gave it two chances. We just couldn't draw the audience needed to justify a third round. We hope we'll get to work with him again."
Watch This Tonight — See why Hannibal is today's editors' pick: