The synagogue was closed in 2007. The congregation, reduced to around 20 regularly attending members, was sharing facilities with a congregation on Henry Street. The Lower East Side Conservancy was trying to raise an estimated $4.5 million for repairs of the building, with the intent of converting it to an educational center. In December the leadership of the synagogue under Rabbi Mendel Greenbaum filed a “hardship application” with the Landmarks Preservation Commission seeking permission to demolish the building to make way for a new residential development. This application was withdrawn in March 2013, but the group Friends of the Lower East Side described Beth Hamedrash Hagodol's status as "demolition by neglect". The abandoned synagogue was "largely destroyed" by a "suspicious" three-alarm fire on May 14, 2017.