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Philip might have hoped that the Armada, having conquered Ireland, would be able to follow it up with a speedy assault on England, but he was soon disabused of that notion. A letter from Medina Sidonia arrived in October informing the king that "between the damages suffered to your fleet, the casualties among your men, and of course the task of integrating Ireland into His Most Catholic Majesty's domains", he did not expect to be able to resume the "Enterprise of England" until the spring of 1589 at the earliest.

Medina Sidonia was not exaggerating. The actual conquest of Ireland had seen few Spanish casualties, most from disease or desertion rather than combat, but the crossing had taken its toll. Many of his ships, especially the galleys, were in poor shape. And with the destruction of Dublin and most of the records of the English administration of Ireland, he was building his new government nearly from scratch.

Fortunately, Medina Sidonia was truly a skilled organizer. He immediately set to the task of expanding Port Láirge's shipyards to handle the task of repairing the Spanish ships. He established two new forts to guard the entrance to Port Láirge - Fort Philip and Fort St. Patrick - and equipped them with cannons taken from some of the damaged Spanish ships. To replace the lost crews, he moved Spanish and Portuguese sailors from those ships that were most damaged onto others. The damaged ships would be recrewed by Irish sailors, ensuring that the crews of each ship would share a language, and formed a new squadron, the Squadron of Ireland, under the command of Gráinne O'Malley.

He also began organizing Irish troops, arming them with Spanish weaponry, and training them in Spanish tactics. These troops would not only assist in the conquest of England, but serve as the core of a permanent Irish army. Medina Sidonia suspected that even after Spain conquered England, it would have to deal with many a rebellion there, just as England had in Ireland, and anticipated that having a large, well-trained body of Irish troops might be useful for suppressing such rebellions. He even sent a letter to Philip, proposing that the Army of Ireland could substitute for the army in Flanders given a few years to train and arm them, but Philip killed that notion. He was already displeased by the delay resulting from Medina Sidonia's Irish gambit. "Every day that you delay the Enterprise, the devil sinks his claws deeper into England, and the heretics continue to practice their foul depredations against the faithful on that island." Even with the necessity of sailing to Flanders, the reduced crossing time from Ireland would make it easier. The fleet would need fewer provisions, and could carry more shot and powder.

For the administration of Ireland, Medina Sidonia turned to the Church. Under the direction of Father Thomas Vitres, the Irish priest who had accompanied the Armada, an Irish bureaucracy grew in Port Láirge, staffed primarily by Irish priests and monks. The Irish churches and monasteries had their own records, and those were used by Medina Sidonia to get a picture of the current state of the island. From this, he began the arduous process of regularizing Ireland's system of noble titles.

Dealing with the Anglo-Norman nobles was relatively simple. Those who had not fled or been killed in the fighting were required to swear fealty to King Philip. Few who had remained refused, but many titles were attainted. For now, King Philip would personally hold those titles, but stated his intention to give them out "to reward those who distinguish themselves in the Enterprise of England".

The Irish titles were more complex. In December, King Philip issued a decree confirming that the ancient brehon law would continue to apply within Ireland. However, he was particularly concerned by the way that many Irish owed their true allegiance not to the lord who had title over their land, but to the head of their clan (the "chief of the name"), and (likely prompted by advisors) suggested that Medina Sidonia see that the chiefs of the name were the Irish nobility. To that end, Medina Sidonia (who was rapidly learning Gaelic) decreed that all Irish nobles be known as chief (ceannaire) or high chief (príomhfheidhmeannach), and would be ranked equal to a viscount (vizconde) or count (conde) of Spain.

In one particular dispute, Turlough Luineach O'Neill, head of the O'Neill clan, claimed the High Chiefdom (formerly Earldom) of Tyrone, which was currently held by his rival, Hugh O'Neill. Both had supported the Spanish takeover, but now they threatened to come to blows. Eventually, Medina Sidonia negotiated a compromise, where Turlough was confirmed as High Chief of Tyrone, in exchange for Hugh being confirmed as his tanist (successor) both as High Chief of Tyrone and head of the O'Neill clan (or "the O'Neill"), with the two titles now being coterminous. As compensation, Hugh O'Neill was granted command of the Irish troops being trained to accompany the Armada, and was privately promised a title of his own after the conquest of England. Gráinne O'Malley was confirmed as Chief of Umhall, and Cormac O'Hara became Chief of Luigne.

On January 12, 1589, the Cúirteanna of Ireland assembled for the first time in Port Láirge. Like the Spanish Cortes on which it was modeled, the Cúirteanna had little real power, but served as a forum for the Irish nobles. Among the first acts of the Cúirteanna was to formally abolish the Irish Parliament (to which it was a successor), and to prohibit all forms of Protestantism within Ireland. In truth, the Irish Inquisition found few actual heretics to burn, and was instead called upon to serve the priest-dominated Irish bureaucracy. The Cúirteanna did play an important role in establishing an Irish judiciary and appointing Irish sheriffs, even if it often had to use Spanish troops to maintain order.

With Ireland's administration coming together, Medina Sidonia returned his attention to the Armada. By February, the final repairs were complete, and the Armada was back at full strength. Drawing on the lessons of the 1588 campaign, supplies were assembled at Port Láirge. In March, Hugh O'Neill marched his Irish troops from Ulster to Port Láirge. On April 23, 1589 - the feast day of St. George - the Spanish Armada set sail once more, now bound for Flanders - and for England…