September
It took him an entire day though since the harbour was difficult to navigate on account of its many shoals. Hendrikzsoon had much respect for the artillery of the castle since they fired heavily and managed to kill 4 of his men on board his vessels. The commander of Castle Morro reported less favourably on the accomplishments of his artillery. Due to bad supplies and insufficiently experienced soldiers he was unable to prevent the entry of any of the vessels. Neither was any of the 17 vessels sunk by the cannon of the Castle Morro.
Most of the inhabitants of San Juan were able to leave the city in time because the Dutch vessels had such difficulty navigating through the harbour. After landing his troops he took the empty city of San Juan. The inhabitants of the city as well as a number of soldiers had taken refuge in the woods nearby. The commander Juan de Haro and some soldiers decided to defend Castle Morro against the Dutch invaders. Haro immediately sent two letters requesting assistance as well as supplies to Spain, via Santo Domingo, and to Havana. In both his letters he stressed the fact that his cannon were in bad shape and that he lacked good quality gunpowder.
On 25 September Juan gave orders to Captain Alonso de Figueroa that he should go inland to gather supplies as well as soldiers for the defense of Castle Morro. Don Antonio de Mercado y Peñalosa and his garrison of 25 men retreated to the tower, called Cañuelo, at the mouth of the river Bayamon. In the middle of the night he and his men managed to sail to Castle Morro unhindered by the Dutch vessels.
On 26 September Hendrikszoon and seven or eight hundred of his men went on shore and marched to San Juan. The Dutch Flag was put up above the House of the Governor and then the Church of the town was plundered. Guard details were posted at strategic points in the city and in the evening much of the wine that was in the city was thrown away to prevent drinking among his men. 4 cannon were taken of the vessels and deployed to cover the Castle. A barricade against musket fire from the Castle was put up. Two squadrons were sent to take the land bridge that connected the island to Porto Rico to prevent attacks from that side. 
The Bridge was destroyed and the guardhouse was occupied. It was decided that Castle Morro would be shot at simultaneously from the side of the City and from the sea-side by vessels. Hendrikszoon received information from prisoners about the bad condition of the supplies and cannon at the castle. The tower on the small island Cañuelo on the West side of the Harbour was also captured. This was a major blow to Juan de Haro because it threatened the main route for supplies to Castle Morro.
The captain of the yacht West-Cappel was ordered to patrol the sea near the harbour in order to prevent supplies from reaching the castle this way.
On 30 September Juan de Haro sends gunpowder and shot to Figueroa together with the request to send supplies to the castle in a manner that is inconspicuous: at midnight with a small boat. He also suggests that the cattle on the island should be driven inland instead of butchering the animals to prevent them from being eaten by the Dutchmen.
October - first half
On 4 October 36 Dutchmen were attacked on the beach by Spanish forces who were able to kill 6 and wound 7 men. Afterwards 3 more men died of their wounds. A chaloupe with cannon and muskets was also attacked that day and, because the captain and his men were drunk, easily captured by Spanish soldiers. All Dutchmen were killed except 3 who managed to jump overboard and swim to safety.
On 5 October the Spanish soldiers of the castle attempted to attack the Dutchmen stationed in the approches near the castle. The Spanish force consised of 40 soldiers. Most Dutchmen saw them coming and managed to escape except one of them who was captured and 11 men who were killed. Among those killed was the Dutch Captain Useel. The prisoner was unable to tell Juan de Haro much about the plans and fortifications however. On this day another boat of the Dutchmen, sailing near bridge to the mainland of Porto Rico, was captured and all in it slain. Only one of the sailors managed to escape by jumping overboard and swimming to safety.
Again Haro sends a request to Figueroa for supplies. He also suggested a plan of attack: a combined attack of Haro and his men from the castle and Figuero from the other side of the city at the head of 100 men. These plans were never carried out, however, because of disagreements regarding the command of the troops. From letters dated 6, 8 and 12 October it is clear that Haro and Figueroa had plans to recapture the island Cañuelo, but abandoned these plans much to the amazement and anger of Haro.
On the night of 6 October Haro and his soldiers again made several sorties from the castle against the Dutchmen in the trenches. They were forced to keep a constant lookout for these suprise attacks. In all about 10 Dutch soldiers were killed. One of the Spaniards, Juan Acensio, showed much bravery during the attack and killed several personally.
Two boats were sent to the harbour to prevent supplies from reaching the Castle on 7 October. This day a Spanish soldier was captured. The Dutch continued to fire their Cannon at the Castle Morro which resulted in heavy damage to the walls. They were even able to destroy a small tower of the Castle. What the Dutchmen lacked for their attack, though, were engineers or mining-engineers. That was why they were unable to create an opportunity to approach the castle and overwhelm the defenders. Another small tower was destroyed by the continued bombardment on the following day, 8 October. On October 9, Hendrikszoon sailed with several ships and was able to destroy 5 cannon of the castle. At night, on the same day, the Vice-Admiral of the Dutch fleet, Adriaen Claesz., sailed with 5 vessels up the river Bayamon. They found 4 or 5 abandoned houses which they burned to the ground.
October - second half
Again two vessels were sent on October 17 to try to retake Cañuelo. One of the vessels managed to disembark its soldiers at the island but they were all killed by the Spanish soldiers barring one heavily wounded Dutchman. He managed to escape to the other vessel that was able to get away despite its crew being halved by the fierce resistance by the Spanish soldiers.
Hendrikszoon had lost a lot of men during the siege of Castle Morro and Tropical diseases had also ravaged his troops. Hendrikszoon also thought it likely that relief forces from Spanish colonies would be arriving sometime soon. The supplies of ammunition of Hendrikszoon and the number of soldiers available were steadily diminishing. Since the vessel Enckhuysen (which still had many of both) was lost to them and since there would be no help forthcoming from The Netherlands, General Boudewijn Hendrikszoon decided to abandon the siege on 18 October.
On 19 October some goods from the city San Juan and two captured cannon were tranported on board the remaining Dutch vessels.
On 20 October Juan de Haro again urged Figuero and his men to attack the Dutch forces. He suggests an attack from four sides using the sloops that were available. Hendrikszoon sent a letter to Haro on 21 October demanding a ransom for the city San Juan which he threatened to destroy. The Spanish commander refused saying that the island had enough wood and stone to easily rebuild the city should this prove necessary. The city was set afire by the Dutch on 22 October when they left the island and went aboard their vessels. The Spanish soldiers immediately deployed cannon along the coast and began shooting at the Dutch vessels. During the next few days the waters were again sounded to search for a safe route to sail out of the Spanish harbour.
November
Again one vessel, the Medenblick, ran aground. The other vessels continued to sail away. When the vessels were out of range of the Spanish cannon they had to stop to repair the leaks due to the Spanish cannonballs. Meanwhile five small boats were sent to the Medenblick to help get it free again. They managed to free the vessel but due to bad management and confusion it ran aground again. At this time Hendrikszoon considered abandoning the vessel because of the fierceness of the bombardment by the Spanish cannon. One salient detail was the fact that one of the Dutch prisoners helped with firing of the Spanish cannon.
In the end he decided to leave with most of the fleet for the West-coast of Porto Rico. On 7 November he arrived in a bay with his fleet and immediately began repairs again. He had ordered three vessels to help and protect the Medenblick until it was freed again. These joined him there on 12 November. The Medenblick had been abandoned by its crew. The part of the crew who was responsible was punished for failing to retrieve the cannon on board the Medenblick. The vessels brought a small Spanish boat with them that had been captured near the coast (Sierra Gorda) on 10 October.
The number of Dutchmen who were taken prisoner was 16. One of these was sent to Diego de Acuna at Santo Domingo. The other 15 were executed.