Much of El Salvador was home to the Pipil, the Lenca, Xinca, and Kakawira. The Pipil lived in western El Salvador, spoke Nawat, and had many settlements there, most noticeably Cuzcatlan. The Pipil had no precious mineral resources, but they did have rich and fertile land that was good for farming. The Spaniards were disappointed not to find gold or jewels in El Salvador as they had in other lands like Guatemala or Mexico, but upon learning of the fertile land in El Salvador, they attempted to conquer it. Noted Meso-American indigenous warriors to rise militarily against the Spanish included Princes Atonal and Atlacatl of the Pipil people in central El Salvador and Princess Antu Silan Ulap of the Lenca people in eastern El Salvador, who saw the Spanish not as gods but as barbaric invaders. After fierce battles, the Pipil successfully fought off the Spanish army led by Pedro de Alvarado along with their Mexican Indian allies (the Tlaxcalas), sending them back to Guatemala. After many other attacks with an army reinforced with Guatemalan Indian allies, the Spanish were able to conquer Cuzcatlan. After further attacks, the Spanish also conquered the Lenca people. Eventually, the Spaniards intermarried with Pipil and Lenca women, resulting in the Mestizo population which would become the majority of the Salvadoran people. Today many Pipil and other indigenous populations live in the many small towns of El Salvador like Izalco, Panchimalco, Sacacoyo, and Nahuizalco.

El Salvador was home to which indigenous peoples?