Why didn't the Spanish eliminate Muslims in the Philippines?

Recently I was reading an article about Islamic terrorism in the Philippines and that led me to wonder:

In colonial times the Spanish were pretty militantly Catholic: Ferdinand and Isabella drove the last of the Moors out of the Iberian peninsula and expelled all Jews; the conquistadors annihilated all but the most covert worship of the Aztek and Incan gods; and Catholic missions were established even in far-flung jungles and deserts. And that’s not even counting the 100+ years of struggle against Protestants in Europe. But while the Spanish fought hard in the Philippines against local sultanates and converted most of the local population under their direct control, they apparently never saw a need to root out Islamic worship in the backwaters of their East Indies holdings. Given the militancy and orthodoxy of the Spanish Catholics (not to even mention their willingness to use ethnic cleansing), why not? Was their hold there shaky enough that they had to compromise?

They tried, but couldn’t.

Right and just to add to that - Spain “conquered the Philippines” in the 16th century. Only it wasn’t the Philippines of today. They spent literally centuries trying to conquer the mostly Muslim southern islands, only largely succeeding by the late 19th century a little before they lost everything to the Americans. Who themselves then promptly had to fight a second counter-insurgency war against the Moros.

For an understanding of how Islam became embedded in Southeast Asia, there are few better books than Winchester’s Krakatoa.

(Short form: the Dutch overlords didn’t do shit for the widespread destitution and destruction caused by that disaster, while the Islamic nations and leaders came in like the modern Red Crescent.)

Dozens and dozens of islands covered with thick jungle have got to be harder to conquer than the Iberian Peninsula. The locals could see you coming from miles away. Your supply lines would be difficut to maintain.

Also, Spanish–Moro conflict - Wikipedia. By this account, a significant Chinese presence hampered and threatened the Spanish hold well into the 18th century, by which time the era of Spain as a superpower was a thing of the past.

Question answered, thanks all.

And getting back the Peninsula took 800 years (compared with an initial conquest which was pretty much “btw, we are under new management” “oh ok”), and was aided in part by the Muslim domains breaking up into little pieces several times. It wasn’t exactly a cakewalk.

THe Philippines was administered out of the Viceroyalty of New Spain, i.e., Mexico. For two and a half centuries, galleons would cross the Pacific between Manila and Acapulco. Shipping trade goods was of course far more lucrative than ferrying soldiers. Aside from the Moros, the Spanish also had to contend with Chinese pirates, the Dutch, the Portuguese, the British, as well as numerous indigenous revolts. They really only started to get a handle on the Moros in the 19th century, but then the Americans arrived.

The Americans themselves never fully pacified the Moros. Even after the rest of the country accepted American rule after the Philippine-American War, the Moros continued to rebel. And then the Japanese came.