On 30 March the crew established a settlement they called Puerto San Julian.

On April 2 a mutiny involving two of the five ship captains broke out, but it was unsuccessful because most of the crew remained loyal. Juan Sebastián Elcano was one of those who were forgiven. Antonio Pigafetta, an Italian from Vicenza who paid to be on the Magellan voyage, related that Gaspar Quesada, the captain of Concepcion, was executed; Juan de Cartagena, the captain of San Antonio, and a priest named Padre Sanchez de la Reina were instead marooned on the coast. Another account states that Luis de Mendoza, the captain of Victoria, was executed along with Quesada. Reportedly those killed were drawn and quartered and impaled on the coast; years later, their bones were found by Sir Francis Drake.

The journey resumed. The Santiago was sent down the coast on a scouting expedition and was wrecked in a sudden storm. All of its crew survived and made it safely to shore. Two of them returned overland to inform Magellan of what had happened, and to bring rescue to their comrades. After this experience, Magellan decided to wait for a few weeks more before again resuming the voyage.