did it have prison?

Yes it has a jail

Unfortunately, yes. Each mission generally had 2 Fathers and 5 soldiers. These soldiers were generally from New Spain (Mexico) and travelled with the Spanish fleet as they developed garrisons within prime coastal bays. The mission Fathers and soldiers assigned to the missions came from New Spain. The European Franciscan Fathers trained for their Alta California missions at a religious university near Mexico City. Back to the soldiers. Many were Mexican, and they were not treated as well as the Spanish soldiers. They were often under-paid or not paid at all. Many were probably unhappy. Being assigned to a mission, these soldiers were in charge of preventing neophytes from leaving the mission grounds or hunting them, if they did. Many of the missions required neophytes to stay within the mission quadrangle. For neophytes who escaped or caused problems, beatings and floggings were common. In serious situations, those punished were kept in areas which easily have been called a jail.

No. It is a cburch

No.

Continued from your other same question: For those who answer no, they don't understand that the missions were much more than a church. When building the mission quadrangles, the church was only one side of the four sides of buildings surrounding the center court. The other three sides of the quadrangle contained the residences for the Fathers and the neophytes. There were married quarters and families, unmarried men, and a special (often horrible) area devoted to protect unmarried young girls and women. Many died being 'protected' through crowded unsanitary conditions. There were rooms for weaving or leatherwork, whatever the mission specialized in. There were areas for cooking and baking, making candles and soap, etc. Trades were taught. But there were also rooms for soldiers quarters. If neophytes were being severely punished, somewhere close to where the soldiers were stationed, a 'jail' was nearby. Unfortunately, some missions had soldiers who brutally treated neophytes.