On 13 December, the fleet reached Rio de Janeiro, Brazil. Though nominally Portuguese territory, they maintained no permanent settlement there at the time. Seeing no Portuguese ships in the harbour, Magellan knew it would be safe to stop.

The fleet spent 13 days in Rio, during which they repaired their ships, stocked up on water and food (such as yam, cassava, and pineapple), and interacted with the locals. The expedition had brought with them a great quantity of trinkets intended for trade, such as mirrors, combs, knives and bells. The locals readily exchanged food and local goods (such as parrot feathers) for such items. The crew also found they could purchase sexual favours from the local women. Historian Ian Cameron described the crew's time in Rio as "a saturnalia of feasting and lovemaking".

On 27 December, the fleet left Rio de Janeiro. Pigafetta wrote that the natives were disappointed to see them leave, and that some followed them in canoes trying to entice them to stay.