Slavery, especially debt-slavery, was central to Philippine precolonial society. It was common for people to sell themselves into slavery in times of famine or to pay debts, and it was more common for wars to be fought over slaves (that were in scarce supply) rather than land (which was plentiful). However, it's also important to note that the societal roles and lifestyles that slaves led were also extremely diverse. Some of them were mere vessels for human sacrifices, others were more or less sharecroppers on their chief's land, some basically counted as close family in the households of their masters, and there were many that were virtually indistinguishable from freedmen in terms of duties and obligations to the chief. You could stop being a slave by paying your "debt", often in terms of labor hours or shares of your harvest, or your children could marry freedmen in order for their offspring to be "half-slaves" or "quarter-slaves". It would be therefore arguably more accurate to say that "slavery" as an institution was actually a representation for the underlying value of "utang" or indebtedness that glued precolonial Philippine society together.

The Spanish colonial government definitely exploited and abused the native population starting from their arrival in 1521, but they probably did not brutalize them to the extent of what was happening in other colonies like New Spain. The reason for this was that due to geographical distance, the Spaniards were less inclined to send so much manpower and other resources in order to consolidate resource extraction in an archipelago literally two oceans away, when they could accomplish similar results by sailing across only one ocean to their resource-rich and slave-rich American holdings. In comparison, the Philippines' value to the Empire was mostly strategic geography: the port of Manila was a staging ground of the Manila-Acapulco galleon trade as well as the Catholic Church's efforts to penetrate into Asia. Spanish observers also considered the Filipino "indio" to be lazy and unindustrious; particularly in the sense that they never seemed to work hard for the "abundance" of the natural resources that surrounded them. Therefore, outside the walls of Manila, there was not much incentive for the Spanish bureaucracy to expand their influence into the untamed countryside.

Under the Spanish Laws of the Indies, Spaniards were officially forbidden from taking natives as slaves. However, there were still two other main methods of governance of the natives in the Spanish Philippines: the encomienda system and the hacienda system.

The encomienda system worked similarly as it did in Spain's other colonies: the Spanish crown granted encomiendas as rewards to conquistadors for their military service in subduing the colonies. Encomiendas were not grants of land so much as they were grants of actual Indian people to rule over and instruct in the Catholic faith: the estancias or land grants made by the Spanish crown were technically not supposed to be owned in the name of the encomendero. After three or four generations, the descendants of an encomendero were ineligible to inherit the encomienda, with its land and natives reverting back to the ownership of the crown; this would prevent a landed aristocracy from arising in the colonies. Encomenderos extracted polos y servicios from their native subjects, or tributes in the form of wares, money, produce and labor. To aid them in these tasks were the native principalia, former tribal "elites" like datus and their warriors that were loyal to Spain and served as intermediaries between the Spanish colonizers and the native masses.

Similar to their American counterparts, encomenderos quickly became notorious for their brutalization of the natives, especially in pursuit of the bandala or quota of produce from the encomiendas to be sold to the Spanish government. Despite repeated measures from Madrid to curtail abuses, the exacting of tributes was commonly perceived as forceful and excessive, and natives were often worked to death in mines, in building ships for use in the galleon trade or on Spanish military expeditions. Chief among the critics of the encomienda were the Spanish friar orders stationed in the Philippines, who often wrote litanies of complaints to the Spanish Crown arguing that the mistreatment of the natives would not be conducive for their conversion to Catholicism. Eventually, the influence of the friars won out as the encomenderos retreated to the cities to profit off the galleon trade, leaving their lands to revert back to royal authority or to be sold off to natives (against Spanish policy). There were also laws in place up until the mid-18th century that prevented non-official non-clerical Spaniards from residing outside the cities, mainly to prevent the decimation of the native population that had occurred earlier in the Spanish Americas. By 1700, most of the Philippine countryside was nominally ruled through the use of administrative provinces by alcalde-mayors or provincial governors.

Though the alcaldes technically ruled, the friars constituted the most tangible form of Spanish authority in the Philippine countryside, particularly in the use of haciendas. Since the Spanish secular state made little initiative to expand outside the cities, friars filled in the gap and became the de facto rulers over the natives for much of the 17th to 19th centuries. Friar religious orders took over the lands that the encomenderos left, purchased some from the natives or forcibly resettled them via the reducción policy in what would become the first haciendas.

The friar hacenderos did not initially operate on a strict and explicit policy of tribute like the encomenderos. Rather, native peasants were first considered as partners in a joint venture, where friars would provide farmers with seeds and capital in exchange for half of the harvest. However, friars began to consider their advances as loans payable regardless of the amount of the harvest. When the farmer ran into a bad harvest, he mortgaged his land to the friar and became a sharecropping tenant or "kasama". Sometimes, friars would engage in outright coercion by seizing land from natives on the basis of fraudulent land surveys.

On a hacienda estate, a friar was the reigning landlord, with his loyal native principalia assisting him in exacting tribute. The estate was distributed piecemeal to inquilinos, tenants who paid fixed rents in grain and subleased their own lands to their kasamas to work. Friars, principalia, and inquilinos all entitled themselves to corresponding shares of the harvest, leaving kasamas, the ones who actually tilled the land, with the least amount of it. It was hard for pious and/or illiterate kasama tenants to combat their own exploitation with the friars who had education, the backing of the Spanish Crown, and the fate of their souls in their hands. And in line with the conflict between secular and religious Spain, some governors even complained of the unfairness of the friars towards their flock. And when Spain opened the Philippines to world trade in the early 19th century, the initial subsistence farming in the countryside turned into an agricultural surplus economy, with mistreatment of kasamas increasing due to rising rents and general economic exploitation. Many peasants ended up moving to the cities or turning to banditry as a result of increasing inequality in the haciendas. Friars were also abusive in other ways: they charged extortionate fees for baptisms, funerals, marriages and other church activities, discouraged natives from being educated in anything else except rote prayer, and used corporal punishment to punish "impious" subjects.

While this was not technically slavery and/or genocide, it could certainly be argued that it was yet another form of colonial exploitation that kept the Filipino masses in perpetual bondage to land that was arguably rightfully theirs.

Eventually, what started to uproot the agrarian status quo in the countryside was the intrusion of the mestizo class, especially with the influence of the principalia. Chinese immigrants intermarried with members of the principalia and began to acquire their own tracts of land separate from friar influence. These Chinese mestizos eventually became a socioeconomic middle class in their own right, posing a threat to the influence of the friars and eventually, the authority of the Spanish Crown in the Philippines.

You might also like this answer for more context.

Sources:

- Barangay by William Henry Scott

- The Encomienda System in the Philippine Islands: 1571-1597 by Jane Calkins Forster

- State and Society in the Philippines by Abinales and Amoroso

- A History of the Philippines by Renato Constantino

- A Captive Land by James Putzel

- Philippine Indios in the Service of Empire: Indigenous Soldiers and Contingent Loyalty, 1600-1700 by Stephanie Mawson

EDIT: words

EDIT: added stuff on bandala

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EDIT: added stuff on reduccion