MTS also controls the San Diego and Arizona Eastern (SD&AE) freight railway and regulates taxicabs, jitneys, and other private for-hire passenger transportation services.

In 1910, Spreckels was able to force a ballot initiative that amended his charter with the City of San Diego to give him more than 25 years on his leases to operate streetcar service.

[5] The first motor bus hit the San Diego area streets in 1922, operating between National City and Chula Vista.

The Comprehensive Planning Organization (now known as SANDAG), an intergovernmental agency of 13 cities and San Diego County, was established in 1966.

[6] The MTDB stepped in and offered to buy the SD&AE for $18.1 million if the Southern Pacific fully repaired the line.

The MTDB decided to build a relatively low-cost light rail system over the tracks, a new idea for the United States, but one that was well established in Germany.

In August 1980, the MTDB established San Diego Trolley, Inc. to operate and maintain the new light rail system.

Starting in 1986, all of these services begin operating under a single brand, the San Diego Metropolitan Transit System (MTS).

[5][7] The East Line's Bayside extension to the San Diego Convention Center and the Gaslamp Quarter opened on June 30, 1990.

[8] Later in the decade, the South Line was extended to the north, reaching Little Italy on July 2, 1992,[8] Old Town on June 16, 1996,[7][8] and Mission San Diego on November 23, 1997.

The Mission Valley East extension built the only underground station in the system at San Diego State University and inaugurated the third route in the San Diego Trolley system, the Green Line, going from the Blue Line at Old Town east through Mission Valley, San Diego State University, and merging with the Orange Line in La Mesa (and proceeding to El Cajon and Santee).

In 2007, MTS completed a "Comprehensive Operational Analysis" that redesigned the area's bus network for the first time in 23 years.

Over the next five years, all Trolley stations were renovated, making them capable of handling low-floor light rail vehicles that eliminate the stairs into the trains and allow faster boarding for people using wheelchairs.

The trolley began service on July 26, 1981,[18] making it the oldest of the second-generation light rail systems in the United States.

In 2023, the trolley had the highest ridership of any light rail system in the United States, with 38,047,300 annual rides, or about 121,600 per weekday as of the second quarter of 2024.

Routes are operated by private contractors and by the San Diego Transit Corporation (SDTC), a subsidiary of MTS.

The San Diego and Arizona Eastern Railway (SD&AE) is a subsidiary of MTS that manages and leases railroad tracks for freight service.

The Baja California Railroad holds the right to operate over the SD&AE Desert Line in the Imperial Valley.

The For-Hire Vehicle Administration division licenses and regulates taxicabs, jitneys, non-emergency patient transport services, and other private for-hire passenger transportation services provided by contract in the cities of San Diego, El Cajon, Imperial Beach, La Mesa, Lemon Grove, Poway and Santee.

[24][25] The board of directors has 15 members, who are elected officials representing the cities and unincorporated within MTS's service area.