The Bayshore shops maintained all the locomotives on the Southern Pacific's Coast Division which stretched south to Santa Barbara.

The roundhouse continued to service diesel locomotives, but the decline of industry and shipping in San Francisco and along the peninsula led to the closure of the yards in the early 1980s.

The station was fully rebuilt and shifted south as part of the Caltrain Express project to accommodate the four track cross section.

The San Francisco County Transportation Authority adopted the Bayshore Intermodal Station Access Study in 2012.

[13] This study examined several alternatives, and proposed to move the platform south by 150 to 700 feet (46 to 213 m) to lie completely within San Mateo County.

[14][17] In the Geneva-Harney BRT Feasibility Study final report, published in July 2015, all of the near-term alternatives for BRT alignment would use existing streets, connecting the new Geneva-Harney line with T Third at Arleta; the long-term alternatives studied would extend Geneva (with a grade separation and connection to Bayshore) by 2040, making a new intermodal station for bus, light rail, and heavy/commuter rail.