After his retirement as a player in 1992, Oberkfell embarked on a successful managerial career that saw him named Minor League Manager of the Year by "Baseball America" in 2005. He also served as the manager of the New Orleans Zephyrs from January 4, 2007 until June 17, 2008, when he was promoted to the Mets as their first base coach, replacing Tom Nieto. During 2009 and 2010, Oberkfell managed the Mets' Triple-A farm team, the Buffalo Bisons. On January 28, 2010, Oberkfell led the Leones del Escogido to their 13th championship in the Dominican Baseball Winter League as their manager.