The lodge building, designed by architect Julia Morgan, replaced and expanded upon an earlier wooden structure known as the Milpitas Ranch House which was destroyed by fire in the 1920s.

In the 1830s, the mission was secularized and its holdings were divided into at least ten land grants (including Rancho Milpitas, or Little Corn Fields Ranch) given to soldiers and civilians supportive of Mexican government.

Nearby Jolon was established as a gold mining town on an old Salinan village site in 1860, astride El Camino Real, the old road connecting all the Spanish missions in California.

Guests included Spencer Tracy, Dick Powell, Will Rogers, Clark Gable, Herbert Hoover, Jean Harlow, Leslie Howard and Errol Flynn.

In 1957, a serviceman named Bill Runyan painted heroic murals depicting Spanish settlement of the area[5] on selected interior walls of The Hacienda.

[10] In 2004, the National Park Service (NPS) released an environmental assessment draft which identified for further study the Julia Morgan-designed Milpitas Hacienda complex including the swimming pool, tennis court and outbuildings as well as a number of other historic structures on the base and in the area.

The NPS wrote that inclusion of the Milpitas Hacienda in the national park system would offer an opportunity to enhance visitor experience and expand their understanding of the lives and work of Morgan and Hearst.

The NPS described the Milpitas Hacienda as representing the themes "expressing cultural values" and "developing the American economy" for its connection to Hearst and his media empire.

This reversal in status for The Hacienda caused the NPS to re-evaluate its study of title transfer and management options, and to cease environmental assessment.

"[10] Today, the United States Army Reserve operates the base, and a civilian concessionaire is allowed to run The Hacienda as a hotel open both to the public and to the military.