Eager to head for home, da Gama ignored local knowledge of monsoonal wind patterns. As a result, his ships inched north along the coast, anchored at Anjediva island and set out to cross the Indian Ocean on 3 October. While the outward crossing had taken just over three weeks the return trip, sailing against the wind, took more than four months.
After sighting land again on 2 January 1499, they passed the Somali city of Mogadishu without stopping and finally arrived in Malindi on 8 January.
By that point, the expedition was in a terrible state. Roughly half of the crew were dead, with most of the survivors afflicted with scurvy. Without enough men to manage three ships, da Gama had the São Rafael scuttled, and its crew split between the remaining two ships. They set up the last padrão at Mozambique on February 1, were back in Mossel Bay by early March, rounded the Cape of Good Hope on the 20th, and favourable currents saw them off the West African coast by 25 April.
Around Cape Verde, Nicolau Coelho's Berrio separated from da Gama's São Gabriel and arrived in Lisbon on 10 July 1499. In the meantime, da Gama's brother, Paulo, had fallen grievously ill. Da Gama handed the São Gabriel over to João de Sá and remained at his dying brother's side. The São Gabriel reached Lisbon in late July or early August. While the da Gamas picked up a ride on a caravel bound for Portugal, Paulo died en route, and Vasco stopped off in the Azores to bury him. He eventually arrived in Lisbon in late August or early September to a hero's welcome on September 9, having spent the intervening period mourning his brother.
He had been away almost two years, had covered some 38,000 kilometres and returned with just fifty-five of his original complement of one hundred and seventy.