The Market Street Railway had existed on the surface parallel to the subway's alignment in some form since 1860 with services terminating at the Ferry Building.

[3] That plan is nearly identical to the design built 60 years later, including two levels of train traffic and provisions for both overhead and third-rail power delivery, but not accounting for a Transbay Tunnel.

[6] However, the entire tunnel would be owned by the district and it designed Muni's level with features like very long platforms to allow it to be converted to use by BART trains.

[9] Starting on February 18, 1980 and continuing for over a year afterward, Muni replaced surface operations with subway service at all stations in the tunnel.

At that point, there were no plans to maintain the street-running tracks on Market Street, but that changed in the late 1980s after the success of several Historic Trolley Festivals.

Muni's Embarcadero portal opened in 1998, and was not an original part of the subway's plan; this allowed connections to Caltrain's 4th and King Station.

[10] Prior to March 30, 2020, the K Ingleside, L Taraval, M Ocean View, and T Third Street Muni Metro lines ran through the entire length of the subway to its direct connection with the Twin Peaks Tunnel.

[12] On March 30, 2020, Muni Metro service, including trains through the Market Street Subway, was replaced with buses due to the COVID-19 pandemic.

[14] It returned to bus substitution three days later, citing malfunctioning overhead wire splices and the need to quarantine control center staff after a COVID-19 case.