The Mission Museum is in the section restored and reconstructed over 100 years ago by the Franciscan Friars from Zacatecas. The arched portico is 200 years old. The Church, which is part of the Museum, has been standing since 1813.

The Mission Museum houses exhibits relating to the colorful history of San Luis Rey. Its collections include artifacts from Native American, Spanish Mission, Mexican Secularization, and American Military periods.

The Mission museum houses the largest collection of 18th and 19th century Spanish vestments in the United States.

The museum also displays a splendid collection of original art including a few pieces over 300 years old.