Berkeley History and Anthropology major here, specializing in both mission studies and native cultures of California. I’ve done research at mission Santa Cruz and written a lot on the history of California colonization. I’ll attempt to answer your question, as well as add some additional info about the impact of the missions on the lives of native peoples.

The missions were actually set up as a way to convert, educate and “civilize” the indigenous peoples of California as the Spanish conquered the area. They were also there to establish trade towns, but their primary intent was to turn the natives into catholic Spanish citizens who would serve the throne as the empire grew. They were in many ways comparable to work camps. To answer your question directly, the missions did lead to settlement, but it was interrupted multiple times and continued by different groups of settlers. The missions themselves technically ran from 1769-1834 and Spanish people lived there, but there were an excessively higher number of native people than Spanish who inhabited them. Then in 1822 when Mexico gained its independence from Spain, they took over the California territory that Spain had claimed and divided it into huge land grants, which they gave to individuals to settle into cattle ranches. The missions were still there but by then the Franciscan priests running them were viewed very negatively, in part for the violence and brutality they inflicted on the native peoples, so from 1822-1836 they were all confiscated and (figuratively) dismantled by the Mexican government (the missions are still physically there and serve as museums today). The ranching areas grew into little towns as white settlers began arriving from the east and from Europe, and when the gold rush hit in 1848 the population in California boomed. The US acquired California the same year.

Contrary to the narrative that the world was told until recently, the native people suffered immensely in the mission system. The Spanish viewed the natives as a source of labor, and lured them to the missions with promises of free food and protection; the problem was that once they were there they couldn’t leave. Many people joined their families at the missions out of fear of the Spanish and the weapons the possessed. They were fed a Spanish diet was very different than the food provided by their usual hunter-gathering ways of life. This also meant they began to eat foods that were foreign to their systems, which lowered their immune systems and contributed to the illness that spread throughout the missions. People died from all types of diseases they had never been exposed to before, as well as malnutrition and exhaustion from being overworked. There are also records of horrendous physical and sexual abuse committed against the people by the priests. It’s currently estimated that over 38,000 native Californians died in the missions system, and even more died outside due to Spanish warfare and loss of their communities who supported them.

In some cases the captive natives revolted, such as in San Diego where they burnt the mission to the ground. In other areas the Spanish had more success in their settlements and the missions lasted upwards of 50 years. Recent evidence from missions Santa Cruz and Santa Clara show that the people held there resisted in ways previously unknown— resisting the religious conversion, continuing to hunt and gather in secret to supplement their diets and visiting/trading with people of their tribes who were able to avoid the missions. Some even broke away and formed their own new tribe of refugees and escapees halfway between Santa Cruz and San Francisco.

Today, many native groups still exist in the area and are forming movements to bring awareness to the injustices of colonization, and are working to reestablish their traditional ways of life. If you’re interested in learning more about their culture and efforts I encourage you to check out this website: http://newsfromnativecalifornia.com/

TL;DR The Spanish settlements were not permanent, but they led to other settlements that were. The most lasting impact of the mission system is what happened to the native population and cultures.