Mr Soares was prime minister between 1976 and 1978, in the aftermath of the Carnation Revolution that ended decades of right-wing dictatorship.
A Socialist, he returned as PM in the early 1980s and served as president between 1986 and 1996.
He had been admitted to hospital in Lisbon last month following a "general worsening of his health", doctors said.
He had shown signs of improvement, but later fell into a deep coma from which he never recovered. The hospital, however, has not revealed the exact cause of death.