There were a number of reasons for the decline of the missions system. The Spanish government grew weaker in time because of rebellions in many of its colonies. They discontinued to fund the missions in California.
There arose numerous rebellions and protests by Native Americans as they began to feel that the mission system was a form of subjugation and slavery.
The independence of Mexico was another major reason for the decline of the mission system. With Mexico's independence from Spain, the government ended the mission system by introducing secularism.
