The Young Ladies' Seminary of Benicia opened in June 1852, the first Protestant Christian school of its kind in California. Mrs. S. A. Lord served as its inaugural principal, followed the next year by Miss J. M. Hudson. In 1854, Mary Atkins purchased the school and transformed it. Born July 7, 1819, in Jefferson, Ohio, Atkins brought an educator's discipline to a frontier town still finding its footing. At its peak, the seminary enrolled 149 students from across Northern California, offering the kind of structured academic program that barely existed west of the Mississippi. The school occupied a site on West J Street that would later be designated California Historical Landmark No. 795, recognized on September 6, 1964. A historical marker placed by the Benicia Old Timers Committee in 1937 still marks the spot, a quiet reminder of what once happened there.

After the Mills purchased the seminary in 1865, they continued operating it in Benicia for six years. In July 1871, the entire institution migrated to Oakland by train. The relocation was a logistical feat for its era: students, faculty, books, furniture, and supplies all traveled together to the new campus. Mills College received its charter from the State of California in 1885, growing into a nationally recognized private college that would endure for over 150 years before merging with Northeastern University. The Benicia building passed to Reverend Charles H. Pope, pastor of the First Congregational Church, who continued running a young women's seminary at the site. In 1873, Miss Mary Snell took over as manager, operating the school with her sister. The seminary celebrated its 25th anniversary in June 1877, by which point Mary Atkins, now Mary Atkins Lynch, had married John Lynch, who served as U.S. Surveyor General for Louisiana.

The connections radiating from the seminary's orbit produced remarkable lives. Reverend Samuel Weyler, pastor of the First Congregational Church of Benicia from 1896 to 1898, had been born a Russian Orthodox Jew in 1863. Working at a store in Kishinev, he befriended a Russian Orthodox priest named Faltin and converted to Christianity. Weyler left Russia for Wurttemberg, Germany, then passed through Ellis Island on July 13, 1882. He attended Chicago Theological Seminary and Knox College in Galesburg, Illinois, then Yale Theological Seminary. From there he served as a missionary in Pueblo, Colorado, pastored a church in Denver, and started Union Congregational Church in Buffalo, Wyoming, before arriving in Benicia. There he founded The Classical Academy, which eventually became Benicia High School. Weyler died on February 8, 1898, at just 35 years old, having crossed half the world and founded a school in the final two years of his life.

Another pastor connected to the church, Reverend Samuel Hopkins Willey, helped found what became the University of California. A Dartmouth graduate, Willey had served as chaplain of the 1849 California constitutional convention before arriving in Benicia. He co-founded the College of California, serving as its vice president from 1862 to 1869, and launched The Pacific, the first religious newspaper on the West Coast. The First Congregational Church of Benicia itself was founded in October 1865, its first services held in Sages Hall above a town saloon. Seventeen charter members voted to adopt the Articles of Faith and Covenant on June 5, 1866. The congregation built its church at 35 West J Street for $6,800, debt free. In January 1961, it changed its name to Community Congregational Church. From a seminary that cost five thousand dollars emerged a college, a high school, a university, and a community of faith that has endured for over 160 years.