[3] The transit center was closed for repairs in September 2018 after cracks were found in structural beams;[4] services resumed in July and August 2019.

The structure has four levels: the ground floor with entrances, retail space, ticketing, and Muni/Golden Gate Transit boarding platforms; the second floor with retail space, food hall, offices, and Greyhound ticket counter and waiting room; the bus deck with bus bays surrounding a central waiting area; and the 5.4-acre (2.2 ha) rooftop park.

A pedestrian tunnel was planned to be constructed below Beale Street to Embarcadero station, connecting the Transbay Transit Center with BART and Muni Metro.

Initially there were five artists included in the program: James Carpenter, Julie Chang, Tim Hawkinson, Jenny Holzer and Ned Kahn.

[14] In June 2017, SFAC and TJPA announced the planned Hawkinson installation would be cancelled as "the nature of the materials, the sculpture's size, and its location" made it "a particularly complex engineering task.

In 1995, Caltrain agreed to study extending its commuter rail service from its Fourth and King terminus closer to the Financial District, including whether the obsolete Transbay Terminal should be removed, remodeled, or rebuilt.

In November 1999, San Francisco voters adopted Proposition H declaring that Caltrain shall be extended downtown into a new regional intermodal transit station constructed to replace the former Transbay Terminal.

[6] In 2006, developers agreed to a new Mello-Roos tax district in the area surrounding the Transbay Transit Center in order for permits for higher buildings to move forward.

[26] The first phase of construction consisted of the aboveground bus terminal, including retail spaces and the rooftop park, plus the concrete shell of the underground rail levels.

[32] As originally planned, the Transit Center was anticipated to be complete by late 2016, with bus operations expected to commence by August 2017.

[45] The transit center was abruptly ordered closed on September 25, 2018—six weeks after opening and during Salesforce's annual Dreamforce conference—following the discovery by workers installing the final ceiling panels of a “major crack” in a steel beam supporting the bus deck above Fremont Street.

[48] The following day, a second, parallel beam was also found to be cracked, causing the transit center and Fremont Street to remain closed at least through the end of the following week.

[51] A Metropolitan Transportation Commission (MTC) peer review panel investigated whether the cracks may have been caused by flaws that developed in the steel during fabrication, plus by stress concentrations arising from weld access holes or weld termination holes cut into the beams, that were added after the shop designs were submitted for approval.

In February 2019, the TJPA announced that it expected repairs to be completed in June 2019, but cautioned that the center would not reopen until the MTC peer review panel published its final report.

[53][54] In April 2019, it was determined that the cracks were caused when crews welding the beams together skipped a crucial step—mandated by the building code—that led to tiny micro-cracks forming.

[55] The facility is under warranty for two years "after substantial completion", placing financial responsibility for the issue on contractors, Webcor Builders and Obayashi Corporation, and their subcontractors.

[56] The beams were fabricated by Herrick Corporation in Stockton as part of a $189 million contract between Skanska USA Civil West of New York and the TJPA.

[57] Muni and Golden Gate Transit buses resumed using the surface bus plaza on July 13, and the full facility reopened on August 11.

[58][59] The park has been criticized for allowing a commercial company to own the naming rights, as well as not having enough bike lanes connecting to other major transit routes.

[60] In September 2018, just a month after the transit center's opening, the TJPA revealed that the walkway around the rooftop park, made of decomposed granite, had begun to deteriorate much faster than expected.

[69][71] As of January 2020[update], Amtrak Thruway buses also use a surface stop outside the terminal — despite previous plans to use the bus deck — due to disagreements between the TJPA and other agencies about costs.