Hendrikszoon judged it unlikely that he could retake it again and set sail again with his fleet on 1 August after having joined up with several other vessels. On 14 August he sent the yacht Duyfken home to report on his progress. His fleet arrived at the island Bequia (island south of St. Vincent) on 29 August. After taking in refreshments he set sail again on 10 September. The course he set took him passed Dominica (12th) and he put in at the Virgin Island Gorda on 19 September to refresh his crew and refit his remaining vessels. During the voyage his fleet was split up by a storm. He arrived with 13 vessels at Gorda, but was joined by the 4 remaining: vessels Geele Sonne, Goude Sonne, de Vlissinghen and a hired vessel.
Hendrikszoon resolved to attack and capture Puerto Rico to make it a base of operations for the Dutch in the Caribbean. On Wednesday, 25 September, he arrived at its harbour. Despite heavy shooting by the cannon of the Castle San Felipe del Morro, that overlooked the harbour and the city of San Juan, he managed to sail into it and land his troops.
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.
Afterwards he laid siege to the Castle Morro and raided the coasts of the island. He did not succeed in taking the Citadel that dominated the city, however. He spent over 1 month trying to take the Citadel during which many of his men were killed. Malaria and other diseases also ravaged the Dutch forces during their stay. In the end he was forced to give up the siege and left on 2 November 1625.
After Hendrikszoon left the harbour of San Juan he sailed to the bay of San Francisco (20 miles from San Juan on the coast of Porto Rico) where he spent an entire month repairing his damaged vessels. During his stay he sent some men to get supplies and water but they were prevented from doing so by the inhabitants of San German. 2 vessels, Koninginne Hester and Jonas, were loaded with prizes that were captured and sent home to the Netherlands (they arrived there in May of 1626).
5 vessels were sent to Sant Domingo to attack and plunder it, but being forwarned, the Spaniards managed to defend themselves very well. After having failed they returned to the fleet again at the island Saona. The fleet set out west along the coast of Santo Domingo but fierce winds drove it back to the bay of San Francisco where it arrived on 2 January 1626. They did managed to capture two Spanish merchants though. After transporting the cargo aboard their own vessels they set fire to them. The crew were sent ashore on Santo Domingo.
While again repairs were made to the vessels two hundred men were sent ashore to scout out the area for supplies etc. They could not find much and returned to the fleet. On 16 January the fleet set sail for the Leeward island Dominica where it arrived on 16 February. The fleet was split up and sent to scout the area. Afterwards the fleet went on and sailed past Guadeloupe, Martinique, Santa Lucia and Granada.
They sailed past de Cabo de Tres Puntas (North-East coast of Venezuela) and arrived near the Island Margarita on 22 February. They decided to attack the castle from the Land-side (which was less well defensible) and after a fierce battle it was taken. On 27 February the fleet sailed away again to the island Cubagua. After exploring the island the fleet went to a harbour near the city of Cumana where they arrived at the beginning of April. The soldiers that were sent on land were attacked by Spanish soldiers. Several were killed and 7 were taken prisoner. They went on to the Island Aves (near Bonaire) where they resupplied their vessels with wood and meat (from captured sheep) and set fire to some houses. The day before leaving the island on 17 April 11 prisoners were set free on the island.
After capturing a rich Spanish merchant vessel, laden with tobacco and wine, the fleet set out for Hispaniola and from there went on to the West point of the island. On 29 April they were joined there by two vessels that were commanded by Captain Lucifer and Geleyn Stapels.
The fleet set sail again on 3 May and was forced, by currents and the wind, to sail along the Northern coast of Jamaica instead of along the Southside. During the stay of the fleet at Jamaica they were joined by vessels under the command of Captain Bankert. He had been sent earlier on a reconnaissance mission to Hispaniola. While in the area he had taken three prizes near the island Mona.
The fleet set sail on 15 May. It sailed past the Cayman Islands arrived near the Isles de Pinas. Several small Spanish vessels were captured and from a prisoner Hendrikszoon learned that both fleets from Honduras New Spain had not yet arrived at Havana. He decided to wait around in the hope of finding either fleet. On 13 June the fleet arrived at Porto de Cabannas (West of Havana). They captured dozens of pigs near the area and destroyed the pigfarm where they were kept. The fleet left the harbour again on 17 June. During the slow voyage along the northern coast of Cuba 4 more Spanish vessels were captured. Hendrikszoon was waiting for the Spanish treasure fleet to attempt to capture it. When the fleet arrived at Havana the found the harbour guarded by 7 Spanish vessels. Apparantly the people thought Hendrikszoon intended to attack the harbour but this was not the case. His men refused to attack because they were low on provisions and wanted to return home.
On 26 June Boudewijn Hendrikszoon became ill and came down wih a fever. After less than a week he died on 2 July.
The fleet sailed along for a while but the crew on board the vessels increasingly began to insist on returning to Holland. Finally the commanders of the fleet gave in and on 12 June the fleet set sail for home. In August of 1626 the fleet arrived there. In the end the spoils were insufficient to recoup the West India Company for their losses and for the fitting out of his fleet.