The first garrison was encamped in tents, but construction began in 1901 on the first of several permanent buildings.

Over the next decade, the army built many new state-of-the-art fortifications, including the Mendell and Alexander Batteries and buildings including barracks, officers’ residences, a post headquarters, and a 12-bed hospital. Most of the original Fort Baker buildings were designed in the Colonial Revival architectural style, which is often characterized by large, stocky symmetrical buildings with classical elements, such as columns, wrap-around porches and decorative windows.

The soldiers’ barracks represented the army’s new interest in providing its soldiers with a healthier environment. Unlike the dark, cramped and often infested 19th century frontier barracks, the large and well ventilated barracks at Fort Baker provided clean running water, ample interior space and modern, indoor toilet facilities. The post also contained important recreational facilities like a gymnasium, a reading room, a post exchange (which functioned as both a small-scale store and lunch room), and even a bowling alley.
 
In 1910, the Fort Barry military post was established and by the 1930s, Fort Baker, Fort Barry, and eventually Fort Cronkhite became part of the Harbor Defenses of San Francisco.

During World War II, the Harbor Defenses of San Francisco, tasked with guarding the harbor with underwater minefields and shore batteries, constructed a mine depot at Fort Baker.

By 1942, Fort Baker included some 159 buildings, after World War II, it was decommissioned as an active military post, but was retained by the army as part of the Presidio of San Francisco, which continued to utilize many of the buildings.

The final uniformed soldiers left the Presidio of San Francisco and Fort Baker when the 91st Division (Training Support) and an Army Reserve unit, moved its headquarters from Fort Baker to Parks Reserve Forces Training Area in Dublin, California.