San Carlos Borromeo is believed by many to be the most beautiful of all California missions. It is here that Fr. Serra made his headquarters for his California missionary work, and where he was buried upon his death in 1784. A year after its founding, the mission was moved from Monterey to a beautiful site in Carmel Valley. The Monterey site was not only inadequate for growing crops, it was a long way from where the Native Americans resided.

Fr. Serra was buried in the sanctuary beside the altar in the adobe church next to his longtime friend Fr. Crespi. A few years later the current large stone church was built around the small adobe church. In 1803, upon the death of Fr. Lasuen, Fr. Serra's successor, he too was buried in the stone church.

When secularization occurred in 1834 all of the mission lands, except the church site, were sold to private parties. The great stone mission church was abandoned and for 30 years stood roofless after its collapse in 1851. Enough money was eventually raised in 1884 to build a new roof, but the steep pitch was out of place with the original design. The latest restoration, begun in the 1930's, has restored a more suitable roof, and is believed to be the most authentic restoration in the entire mission chain.