A permanent garage opened in San Rafael in 1974, and the facility was expanded in 1987 to house additional administrative staff.

Transbay commuter bus service was reduced in 1987 as a result of declining ridership associated with a shift in jobs from San Francisco to Bay Area suburbs.

In 1993, acting on behalf of MTC, GGT began operating service between Marin and Contra Costa counties via the Richmond-San Rafael Bridge.

On June 15, 2009, Golden Gate Transit began operating Route 101,[7] which provides all-day service between Santa Rosa and San Francisco with fewer stops, similar to many bus rapid transit "light" systems that rely on stop spacing changes rather than capital improvements to speed up buses.

Introduced initially as a weekday-only route, service was expanded to Saturdays in June 2010 and to Sundays and holidays in September 2011.

The next day, service began on Route 580,[8] which was the District's first transit line into nearby Alameda County.

GGT buses returned to Alameda County in February 2019 to provide Early Bird Express bus service under contract with BART.

Golden Gate Transit serves cities and communities in four Bay Area counties: San Francisco, Marin, Sonoma, and Contra Costa.

[10] Golden Gate Transit has operated mostly suburban-style coaches fitted with high-back seats, overhead luggage bins, and reading lights since its inception.

Golden Gate Transit charges different fares, depending on distance (zones) traveled and method of payment.

[15] The program required the formation of not-for-profit organizations to collect riders' subscription fees and develop schedules.

The Marin Commute Club, which began service in 1971, had direct service from Marin County to three University of California, San Francisco locations (Parnassus Campus, Mission Bay Campus, San Francisco General Hospital) not otherwise served by Golden Gate Transit.

However, the economic downturn and changing travel patterns resulted in substantial service reductions and fare hikes.