After being reassigned to Mexico, he published the book Sucesos de las islas Filipinas in 1609, considered one of the most important works on the early history of the Spanish colonization of the Philippines.

He also took command of Spanish ships in a 1600 naval battle against Dutch corsairs, but suffered defeat and barely survived.

[2] In August 1593 he was notified that he had been selected as lieutenant to the governor-general of the Philippines, starting what would become 43 years of colonial service.

His first two reports to the Crown covered a wide variety of topics, mentioning Japan, Mindanao, and China, in addition to civil, military and ecclesiastical activities within the colony.

In 1598 he resigned as lieutenant governor to assume the office of oidor, or judge, in the newly re-established Audiencia of Manila.

[3] From his observation of textiles in the Manila inventory, the Spanish were buying: ...raw silk in bundles...fine untwisted silk, white and of all colors...quantities of velvets, some plain and some embroidered in all sorts of figures, colors, and fashions, with body of gold and embroidered with gold; woven stuff and brocades, of gold and silver upon silk of various colors and patterns...damasks, satins, taffetas...[4] Other goods that de Morga mentioned as being exported in the galleon trade were: ...musk, benzoin and ivory; many bed ornaments, hangings, coverlets and tapestries of embroidered velvet...tablecloths, cushions, and carpets; horse-trappings of the same stuffs, and embroidered with glass beads and seed-pearls; also pearls and rubies, sapphires and crystals; metal basins, copper kettles and other copper and cast-iron pots.

.wheat flour, preserves made of orange, peach, pair, nutmeg and ginger, and other fruits of China; salt pork and other salt meats; live fowl of good breed and many fine capons...chestnuts, walnuts...little boxes and writing cases; beds, tables, chairs, and gilded benches, painted in many figures and patterns.

They bring domestic buffaloes; geese that resemble swans; horses, some mules and asses; even caged birds, some of which talk, while others sing, and they make them play innumerable tricks...pepper and other spices.

[5] De Morga closed his inventory list by stating that there were "rarities which, did I refer to them all, I would never finish, nor have sufficient paper for it.

On 1 December 1600, Governor Tello appointed Morga captain general of the fleet, with orders to attack the two Dutch ships.

Unable to fire – the gunports were closed because they were under the waterline, because he had allowed the ship to be dangerously overloaded – Morga ordered the San Diego to ram the Mauritius and grapple it.

Thirty soldiers and some sailors boarded the Mauritius, taking possession of the forecastle and after-cabin and capturing the Dutch standard.

Morga swam for four hours, holding on to the Dutch standard, and made it to a small deserted island, where a few others of the ship's company also arrived.

The artifacts included Chinese porcelain, celadon ware, Japanese katanas, Spanish morions, Portuguese cannons, and Mexican coins.

An MV San Diego warship museum has been constructed on Fortune Island to display and interpret many of the artifacts.

He arrived in Guayaquil on 8 September 1615, having narrowly escaped falling into the hands of Dutch corsairs off the island of Santa Clara.

It was a time of confrontation between the civil and ecclesiastic powers, as well as disputes between the Creole and Peninsular monks for control of the religious orders.

[9] Although Morga was widely known to gamble extensively, have affairs with women, and conduct other questionable activities, he still achieved bureaucratic reforms, as well as of the liturgy, and helped improve treatment of the native peoples.

In 1609, he published the work for which he is now remembered – Sucesos de las Islas Filipinas (Events in the Philippine Isles).

New Spain viceroy Luis de Velasco (hijo) authorized the publication and granted Morga the sole right to publish it for ten years, on 7 April 1609.

The work greatly impressed Philippine independence hero José Rizal (1861–96), himself a man of letters and of action.

He wrote: If the book (Sucesos de las Islas Filipinas) succeeds to awaken your consciousness of our past, already effaced from your memory, and to rectify what has been falsified and slandered, then I have not worked in vain, and with this as a basis, however small it may be, we shall be able to study the future.