In 1946, the City of New York took title to the Washington Street property in connection with the construction of the Brooklyn Battery Tunnel.

The chapel survived the September 11th Attacks and sheltered its inhabitants from harm from the disaster a mere one and a half blocks away.

After the attacks, rescue and emergency staff removed the pews and operated the chapel as a command station.

In 2017, St. Joseph's Chapel was threatened with closure due to the St. Peter's parish's reluctance or inability to pay a tripling of its rent by a management company run by LeFrak corporation and partners.

[7][2] In November 2017, an announcement was made from St. Peter's that despite the community's efforts to achieve a better solution, St. Joseph's Chapel would indeed close in January 2018.