The history of Gloria Dei Evangelical Lutheran Church began on September 25, 1960 when Rev. Robert O. Waldschmidt was installed as a missionary of the Wisconsin Evangelical Lutheran Synod to serve Santa Clara county. Three years later, on June 9, 1963, the constitution of Gloria Dei Church was formally signed and the new Lutheran congregation was established. The current Gloria Dei campus was purchased on January 2, 1964 for $95,000, which was the most that the Wisconsin Synod had spent to purchase land for a new church up to that point in its history. The groundbreaking ceremony for the new church building took place later in the same year on December 20. The building project was formally completed with the cornerstone laying and church dedication service on October 17, 1965. The total cost for the church building project was $45,000.

In 1970, one decade after initial work began to establish the congregation, Gloria Dei opened its doors to establish a Lutheran elementary school. The school opened with eight students enrolled in its inaugural year. Classes were held in the downstairs fellowship hall of the church building.