In 1835, the Presidio was temporarily abandoned when Commandante Vallejo transferred his military headquarters north to Sonoma. By this time, Juana’s husband had become abusive and, with the aid of a local bishop and the mayor, she moved to the western foot of Loma Alta, now called Telegraph Hill. Here, Juana constructed a one-and-a-half-story adobe—the first private house built between the Presidio and Mission Dolores—and held the title in her own name. A savvy entrepreneur, Juana sold milk and vegetables to ships' crews and also served as a nurse and midwife to the growing community. Without formal medical training, she treated smallpox and scurvy patients, delivered babies, and set broken jaws. Juana also continued to employ her knowledge of medicinal herbs; it was said the community of Yerba Buena was named for her healing mint tea.
In 1844, Juana Briones de Miranda purchased a 4400-acre tract of land called Rancho la Purisima Concepcion to further expand her cattle and farming interests. A part of her adobe home still stands on Old Adobe Road in Los Altos Hills in what is now Santa Clara County. When California entered the Union and land holdings had to be confirmed by the United States government, many lost their territorial possessions. Juana, however, was highly respected in her community and was allowed to retain ownership of her property when many others were less fortunate. Juana Briones' later life is well documented, as she acquired several other properties during this time. She died in 1889 and was buried at Holy Cross Cemetery in Menlo Park.
Although there are no surviving diaries, letters, or photographs related to Juana, details of her life are dawn from the accounts of early travelers to the San Francisco Bay area as well as from legal papers, newspaper articles, maps and deeds, and old history books. Her generosity and reputation as a healer established her reputation during her own lifetime, when today's North Beach was called La Playa de Juana Briones. In 1997, the State Department of Parks and Recreation honored her with a plaque at her home site in today’s Washington Square. In Palo Alto, there is a park and a school named for her and the Juana Briones Heritage Foundation and other conservation groups work to preserve her house and heritage in Palo Alto.