By 1811, the mission had grown, and Father Peyri started new a church, the one we see today, 180 feet long, 28 feet wide and 30 feet high. Jose Antonio Ramirez came from Mexico to teach Indians construction techniques for the new church. Completed and dedicated on October 4, 1815, it was built with adobe, lime plaster, wooden timbers and included fired clay bricks and roof tiles.
The building is built in a style called Spanish Colonial, a combination of Baroque and Classical elements. Detailed work on the church continued for ten more years.
By 1826, the quadrangle was 500 feet long on a side. In the front, the convento stretched 600 feet long with 32 arches. It had rooms for priests and guests. The mission also had an infirmary, women's quarters, storerooms, workrooms, orchards and gardens outside. The oldest pepper tree in California, brought from Peru around 1830, still grows in the quadrangle.
In front of the mission are an open-air laundry (lavanderia) and sunken garden. Here, water flowed from two springs through open-mouthed gargoyles (stone faces) into a bricked area where the Indians did the laundry. It then flowed into an irrigation system that watered exotic plants and orchards. The water system even included a charcoal filter purification system to keep drinking water clean.
Today, the mission is restored and re-painted to match pictures of the original interior. The Stations of the Cross painted on the walls were painted for Mission San Luis Rey in Mexico in the 1780s. The wooden pulpit, the only wooden part of the mission to survive termites, is original. The original reredos behind the altar was destroyed by treasure-seekers, and they have not tried to recreate it since no original drawings or pictures survive.