A native of Imus, Cavite, Santiago was the eldest child of revolutionary general Mariano Alvarez (1818–1924) and Nicolasa Virata.

After his birth, his family immediately moved to Tierra Alta, Cavite (present-day Noveleta) where he acquired his early education at age seven under Sr. Antonio Dacon.

Santiago married Maria Paz Granados of Tanza, Cavite with whom he had ten children - Marta, Magdalena, Gabriel, Pacita, Numeriano, Egmidio, Rosendo, Virginia, Amalia, and Fidel.

A notable combatant, Santiago displayed heroism and bravery in various battles within Noveleta, specifically in the towns of Naic, Maragondon, Magallanes, Tanza, Alfonso, Silang, Imus, and Francisco de Malabon.

During the establishment of the American civil government in the Philippines in 1901, Alvarez assisted in the organization of the Partido Nacionalista (1901–1907), wherein he later became president of its directorate.