The great problem of the Spanish administration was the instability of its policy. The Governors were appointed in accordance with the political exigencies of the day in mainland Spain; their average tenure of office was less than 3 years, and the rate of turnover increased towards the end of the period. The turn of events in the Spanish colony was thus usually dictated by happenings in Europe. The 377 years of Spanish rule were fairly eventful years, and the Spaniards were several times on the point of abandoning or losing their colony. The complete conquest of the colony was relatively easy process as well as the establishment of Spanish power.
In 1635, the Spaniards built a fort at Zamboanga on the island of Mindanao and thus established their position in Muslim territory. During this time, the Muslims had already established themselves in the southern part of the archipelago. The less centralized sultanate of Maguindanao and the very powerful sultanate of Borneo were overshadowed by the sultanate of Sulu, over which the Spaniards never achieved complete control; and even the destruction of the town of Jolo by the Spaniards in 1876 did not eliminate the sultan, though it put an end to his supremacy.
Jolo was a great centre of trade which attracted both Chinese junks and Malaysian vessels from Celebes and Java. The Chinese brought metal articles and took away in return mainly foodstuffs (sharks fins, pearls, sea cucumbers). The Muslims obtained supplies by piratical raids on the coastal regions which were now in Spanish hands, and these activities were facilitated by the Spanish practice of establishing settlements round ill defended mission stations. The slaves captured in this way might be sold in markets as far afield as Jakarta (Batavia). Spanish attempts to conquer Muslim territory were bound, therefore, to encounter fierce resistance, since the Muslims could not contemplate the loss of their trade and their slaves, still less of their religion for the Spaniards required the peoples of conquered territory to abandon Islam for Christianity.
A few years later the threat of attack by the Chinese pirate Coxeng obliged them to concentrate their limited forces in Manila, and they did not re-establish themselves at Zamboanga until 1718. In the intervening period they had had to cope with attacks by the Dutch and numerous risings in various parts of the Philippines. Thereafter, Spain was increasingly weakened by the dismemberment of the Habsburg Empire, followed by a series of European conflicts the War of the Spanish Succession, the Seven Years War, etc. The decline of Spain distracted its attention from the Philippines until 1821, when Mexico achieved independence, and culminated in the loss of the Philippines in 1898. As a consequence of the wars in Europe British forces occupied Manila from 1762 to 1764, and this indication that Spain could be defeated encouraged resistance within the country. Only then did the Spanish authorities put through reforms designed to secure more centralized government and strengthen their control of the country. Finally the 1860s saw the beginnings of the nationalist phase in the history of the Philippines.