Jeff and other Wilpon family members invested with Bernard Madoff's ponzi scheme that collapsed in 2008. Unlike many who lost their investments, it was revealed in the Madoff firms court case, In the Securities Investor Protection Corp. vs. Bernard L. Madoff Investment Securities LLC, USBC SDNY No. 08-01789 that the family partnership run by Wilpon made $48 Million dollars in their dealings with the firm. He also is a member of the board of directors for the Holocaust museum in Washington DC.
Wilpon has been criticized by some for being too much of a meddler in the baseball operations for the New York Mets. In 2010, Joel Sherman of the New York Post wrote, "Let’s give Jeff Wilpon the benefit of the doubt here for a moment. Let’s say he is not short-tempered. Tone deaf. A credit seeker. An accountability deflector. A micro-manager. A second-guesser. A less-than-deep thinker. And bad at self-awareness. Fine, he’s none of these things. But here is the problem: This is his perception in the industry as the Mets try yet again to fix their baseball operations department."
Sherman also cited a baseball executive in regular contact with the Mets, who said, “Jeff is the problem with the organization, and he is never going to realize that. He cannot help himself. He has to be involved. He will never hire anyone who will not let him have major input. He will not hire anyone who does not run every personnel decision through him.” An AL executive added, "The only person with a worse reputation than Jeff Wilpon in the game is [Marlins president] David Samson." 
In 2003, the team’s previous partner, Nelson Doubleday, Jr., told The Star-Ledger: “Mr. Jeff Wilpon has decided that he’s going to learn how to run a baseball team and take over at the end of the year… Run for the hills, boys. I think probably all those baseball people will bail… Jeff sits there by himself like he’s King Tut waiting for his camel.”
Many commentators on the internet and in broadcast media have referred to Jeff Wilpon as "Fredo" Wilpon, after the feeble-minded member of the Corleone family played by John Cazale in The Godfather and The Godfather Part II.
- "Sandy Koufax among those swindled by Madoff". Sports Illustrated. February 5, 2009. Retrieved August 13, 2009.[dead link]
- Kamalakaran, Ajay (October 21, 2009). "NY Mets owners made about $48 million in Madoff dealings". Reuters. Retrieved October 21, 2009.