You may be interested to see this declaration made by Bishop Salazar and theologians of the Spanish Philippines in 1591, pertaining to the treatment of native indios in the encomiendas:

Restitution must be made for all tribute taken before any service had been rendered; anything above one-half taken before religious instruction was provided as to be returned.

2. Full tribute should not be collected from infidels who, after hearing the religious instruction, rejected it.

3. Sufficient ministers should be provided so that they might give more individual attention to the converts.4. Encomenderos should not seize chiefs and hold them prisoners until they paid the tribute of all their subjects.

4. Encomenderos should not try to save on expenses by providing too few instructors.

5. Encomenderos should not consider themselves the lords of the Indians, but rather their attorneys, tutors, and protectors. Encomiendas are instituted for the good of the Indians, not the encomendero.

This is of course not to say that Spain had completely benevolent aims for the subjugation of the Philippines: directives of this sort were often ignored by encomenderos, and the conquest of the archipelago in the late 16th-early 17th centuries was so traumatic some islands suffered as much as a 40% population decline. But it is important to note that the Spanish conquest of the Philippines was situated in the context of the American conquests some decades earlier, where colonial brutality led to as much as 90% of the population being exterminated by violence or disease. The Catholic Church in particular was determined to learn from the mistakes of its government in the Americas, where the mistreatment of the natives had not been necessarily conducive towards their salvation in Christ.

It is important to note that in the early centuries of Spanish rule, the Philippines was not necessarily a very profitable colony for Spain. With the addition of the breadth of the Pacific, this meant that not many Spaniards were able to occupy the Philippine archipelago at a time. On one hand, this limited their capacity for further military action and conquest. But on the other hand, this made them paranoid of their own numerical inferiority, as well as exacerbating the need to raid for resources. During the 1500s-late 1600s, the primary mode of Spanish governance in the Philippines was through the encomiendas, which were collections of native "souls" entrusted to former Spanish conquistadors for their service. Much like in America, these encomenderos worked to death much of the natives entrusted to them, in the pursuit of collecting tribute as well as desperately making a profit from a colony deemed unprofitable. And much like in America, the Catholic friar orders were the first to document these abuses and send them to Madrid in protest, from where the king had prohibited that the natives be pacified through war. The friars also tried to separate the natives from their encomendero masters, much to the irritation of the latter. In addition to possible holy zeal, the friars were also motivated by the Islamic threat from the south, from where Muslim missionaries could appeal to disillusioned natives.

In 1581, Bishop Domingo de Salazar arrived in Manila, and his documentation of the abuses of the encomenderos was responsible for the establishment of the Real Audiencia in the Philippines. Established by Philip II in a 1583 secular decree, the Audiencia's prime purpose was to curb the abuses of the Spanish government in the islands and enforce Philip's previous decrees against the mistreatment of the Indians, e.g. the prohibition of their enslavement, the fixing of their tribute so as to be commensurate with their actual economic capacity, and the role of the clergy in acting against abuses. There were investigations of abusive encomenderos with witness statements from friars and native leaders, upon which the accused was to pay a fine as well as restitutions towards native communities for the excessive tribute levied from them. Eventually, encomienda grants in the Philippines started declining in the 1650s and became all but extinct by 1700 as the galleon trade became the prime method of profiteering in the colony. Around that same time, laws were put up restricting nonclerical Spaniards from residing in the countryside, in order to prevent the steep population decline that had happened in the Americas.

Behavior like this on the command of Philip II might seem odd coming from a European colonizing monarch, but remember this is the same man who, upon being advised to abandon the Philippines as a colony, declared that he would sacrifice all the wealth of the Indies just to save one native soul. Like most governments around the world, the Spanish court was filled with a complex variety of motivations: there were the merchants and the conquistadors as well as the zealots and the friars, who saw the wars of conquest as a way to spread the gospel of Christ and save the souls of millions. There were multiple means to bring this message over to the heathen natives, but starving, beating and overworking them would probably not be the most effective among them. And especially in the Philippine context, where Spain had to contend with local superstitions, Muslim and Hindu depredations as well as Imperial China, the Spanish conquerors had to be very careful about competing influences among the natives. Like most other rational people looking to control populations, European colonizers understood very well the nature of the carrot and the stick.

Sources:

- State and Society in the Philippines 2nd. ed. by Abinales and AMoroso

- Conquest and Pestilence in the Early Spanish Philippines by Linda Newson

- Church and State in the Philippines during the Administration of Bishop Salazar, 1581-159 by Horacio dela Costa

- The Encomienda System in the Philippine Islands, 1571-1597

- The Encomienda in Early Philippine Colonial History, by Eric A. Anderson