Hi,

you may be interested in this earlier (longish) answer of mine on a similar question.

In brief: I mention in there how Spanish control was quite secure over the Valley of Mexico by the mid-16th c. Still major rebellions occured throughout colonial times in New Spain - incl. the early Mixton War, but also major resistance in northern regions and the Yucatán.

At the same time, there were also major urban rebellions e.g. in Mexico City, in part by descendants of the Mexica. They were typically not against Spanish rule, but against specific policies or grievances, which were in turn partly influenced by dev'ts in Spain.

Hope this helps!