* Disease: The missionaries also faced a number of diseases, including malaria, smallpox, and measles. These diseases often decimated the native population, and made it difficult for the missionaries to spread their faith.
* Attacks from Native Americans: The San Miguel Mission was also attacked by Native Americans on several occasions. These attacks were often motivated by the Native Americans' desire to protect their land and way of life.
* Secularization: In 1834, the Mexican government passed a law that secularized all of the missions in California. This meant that the missions were no longer controlled by the Catholic Church, and their lands were sold off to private individuals. This had a devastating impact on the San Miguel Mission, which lost most of its land and was eventually abandoned.