WI: Governor-General Juan de Silva defeats the Dutchmen at the Moluccas?

With a POD in the early 17th century who knows if Mindanao is part of the Philippines, if such an entity exists, in ATL 2016?

But to address your question, Ternate and Tidore were both sacked by the Spaniards in 1606. The POD you outlined would mean Spain takes Fort Victoria in Ambon and terminates the alliance the VOC had arranged with the local rulers, cementing Spanish power in the Malukus. But considering Spain's 17th-century position and the issues I outlined above, their role is probably not too dissimilar from the role of the Portuguese in the early 16th century; Spanish naval power and internal Malukun division allow Manila to wield significant regional influence, but there is no spice monopoly. Malukuns retain great independence and Spanish positions are significantly more dependent on local allies than was the case OTL for the Dutch. I think only areas with a large Catholic population, like parts of Ambon (a third of the population of Ambon was Catholic), would be truly loyal to the Spaniards. And there are important challenges to the Spaniards by mid-century: Portuguese independence, Makasarese expansion eastwards, the intrusion of Western Europeans, and various vagaries of history like Koxinga.

IMO it's possible (if not the likeliest possibility) that Makasar would expel the Spaniards from the Malukus. As a major Islamic power, Makasar holds the legitimacy to unite the Muslims of the Malukus against the Christianizing Spaniards (this possibility was why the VOC banned proselytizing to Muslims).[1] And as the largest eastern Indonesian empire in history, it had the capability to take on the Spaniards and have a chance at victory. After all, an Englishman reports in 1615 that when the Sultan of Makasar made ready for war, "at an instant were mustered 36,000 able men."

Hehehe. Well, I mean the same loose category of semi-subjugated sultanates under the Spanish heel rather than the Dutch/British one. And yeah, the Portuguese going free would be a problem.

So, the Maluku islands can, in fact, be kept under Spanish rule and Christianized? Interesting.

From what I understand of the history of Mindanao, it kept on being subjugated but the subjugations kept on not sticking until the Americans and the settling of Visayan landowners via the homestead program all over the island. So really, the majority of Mindanao wasn't Christian until we were well into the 20th century. All that's needed is a loyal Christian minority.

As for Makassar, it sounds very interesting.
 
So, the Maluku islands can, in fact, be kept under Spanish rule and Christianized?
If the Spaniards are lucky, the former is possible for some time (and sooner or later the Malukus will become largely unimportant to the Europeans once Malukun spices begin to be cultivated elsewhere). Christianization is unlikely except in non-Muslim areas, and attempts at Christianization of Muslims will ironically imperil Spanish influence over the Malukus and give Muslim powers (Makasar) or more tolerant Western European Companies an opening to oust the Spaniards.
 
If the Spaniards are lucky, the former is possible for some time (and sooner or later the Malukus will become largely unimportant to the Europeans once Malukun spices begin to be cultivated elsewhere). Christianization is unlikely except in non-Muslim areas, and attempts at Christianization of Muslims will ironically imperil Spanish influence over the Malukus and give Muslim powers (Makasar) or more tolerant Western European Companies an opening to oust the Spaniards.

The former alongside a Christian minority is all that's needed. Though wait, would Northern Celebes be possible as well?
 
would Northern Celebes be possible
The littoral of North Sulawesi was under a loose Makasan hegemony only after the late 1630s, so sure, the Spaniards could have grabbed it for at least some time if they acted fast enough. Spain won't be able to enforce any sort of monopoly on the tortoiseshell trade, so Spanish control over the region might not actually cause that many major commercial ripples (tortoiseshell was the main product of North Sulawesi).

Unlikely. Bali is essentially an extension of Java: a densely populated area with strong Indic influence (so strong, in fact, that Hinduism has survived). The Balinese population was considerable - as many as 500,000, equivalent to the population of Makasar's South Sulawesi heartland and nearly as large as the population of the entire Philippines at the time - and Early Modern Balinese battles often featured armies larger than the entire Spanish population in Southeast Asia.[2] And without the VOC's thirst for Balinese slaves I think it might be possible that Bali is reunified under a single powerful kingdom (OTL, the island collapsed into multiple kingdoms around 1650 and never reunited), making conquest well nigh impossible.

The other places you named are fully possible, though.

[1] In 1636 Makasar conquered Manado and in 1638 Gorontalo.

[2] E.g. the Battle of Buleleng in 1733 featuring 12,000 troops.
 
Better to conquer places with value for the Spanish. In more moderns terms, it is like creating a Gantt Chart for Spanish value conquest based on the ROI.

For this Area it would be Ambon, Northern Sulawesi.

The Spanish did do divide in conquer during the time they came in Luzon. They can technically do that as well in other areas. But I dont think they would conquer by force of Arms after de Silva wins. The Spanish still cannot recruit tens of thousands of troops like they did in the Seven Years War from Luzon when the British tried conquering the colony.

They can always do what they did to Mindanao, stay in Zamboanga, in this case a small enclave, fort until they can force themselves like did come the 19th century or stay away from high lands like what they did to the Luzon highlands.

Spanish would be the dominant Navy, Superpower in the East Indies though until some ambitious European nation comes again.
 
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