The correct answer to this open question is the following.
One of the things that dramatically changed was the conception of spirituality that Native Mesoamerican and Southamerican had regarding God or religion.
One of the first things Spaniard frays did was to evangelize Native Indians into Catholicism. For this to happen, Spaniards face strong opposition from Natives who truly believed in their many gods and deities. It really was a struggle for Spaniards to change their mentality. They even had to destroy Native Indian's temples but had to build churches in the same place to make Indians attend religious ceremonies and religious teachings.
Paradoxically, one thing that stayed the same before and after colonization for native peoples was their love for mother nature. Indians still believed in their deities and in the love and respect they had for mother nature. Even in modern-day Mexico and Peru, there are plenty of people that believe in taking care of nature and use herbs and plant formulas as medicines. Homeopathy is very important in Mexico. And in both countries, Indigenous ceremonies are still performed in most of the towns.