The encomienda system was basically a system employed in Spain to make use of the Native American population and force them to work.
What the system did was promise Native Americans "Protection" from rival tribes as well as others that wished harm for converting to Christianity, following Spanish principles and culture (including language), and working tirelessly for them. Natives were treated like slaves most of the time.
Hope this helped. Let me know if you want me to go a bit more in depth though, and I will edit my answer ^-^