[3] The museum had a small exhibit space at The Cannery (a former Del Monte fruit-canning plant that is now a shopping center) until 2000, when it lost its lease.
[4] It then had temporary exhibits at Pier 45 (near Fisherman's Wharf) and at San Francisco City Hall.
[3] One of the purposes of the merger of the two organizations was to put together a single proposal to renovate and operate the Old San Francisco Mint as a history museum,[5][7] which ultimately did not succeed.
[8][9] Notwithstanding the merger, the Museum of the City of San Francisco's website, operated directly by Gladys Hansen, remained independent and in 2003 renamed itself the Virtual Museum of the City of San Francisco.
[10] Hansen's personal research collection of artifacts from the 1906 San Francisco earthquake also remained in her possession.