Why did the mission system end?
Many forces worked together to bring an end to the mission system. Perhaps the fundamental reason was that the missions had served their purpose as the primary means of "settling" California and transforming it from a wilderness. By 1830s the mission controlled lands covered about 1/3 of the future state, and the total population had grown to about 30,000 - in the missions, presidios and towns that were formed (the most prominent of which would become Los Angeles). As the number of settlers grew they came to covet the lands and property of the missions.
California became part of Mexico in 1821. There was considerable support in Mexico City to end the mission system and the control of these valuable properties by the Catholic Church. Finally in 1831-32 the missions were "secularized" by the Mexican government. Land was distributed to the Indians (most of who were quickly hoodwinked out of their holdings). The major beneficiaries were former soldiers, settlers and others with influence that were given large land grants. Many of the former mission churches became parish churches but some were abandoned and the Indians largely dispersed into the towns and ranches, or moved to the interior.