São Miguel Arcanjo was one of the Jesuit-Guaraní reductions established in the borderlands of the Spanish and Portuguese empires. Jesuit missionaries and Guaraní communities founded an initial settlement in 1632, during a period when slave-raiding bandeirantes from Portuguese Brazil attacked missions east of the Uruguay River. That community moved west for safety. A later São Miguel was established in 1687 as part of the Seven Peoples of the Missions, on lands that now lie in Rio Grande do Sul, Brazil.

The reduction gathered thousands of Guaraní residents around a broad central plaza. The church, council buildings, workshops, school, cemetery, gardens, and family housing followed a plan shared across the mission region. Jesuits pursued conversion and imperial order, while Guaraní people supplied knowledge, labor, leadership, music, farming, and craft traditions. The settlements could offer protection from enslavement and access to livestock and tools, yet they also imposed Christian discipline and reorganized Indigenous space, work, and ritual. Their culture emerged through negotiation under unequal colonial power.

São Miguel's monumental stone church was built principally between the 1730s and 1750s, traditionally associated with the Jesuit architect Gian Battista Primoli. Guaraní masons and artists carved sandstone, made sculpture, performed sacred music, and maintained the complex. The three-aisled church, imposing façade, and separate bell tower expressed both Baroque Catholic ambitions and local workmanship. Surrounding fields and enormous cattle herds supported the settlement's economy, while yerba mate and craft production linked it to regional exchange networks.

The 1750 Treaty of Madrid transferred the seven eastern missions from Spain to Portugal and ordered their Guaraní inhabitants to relocate west. Communities resisted losing their towns and ancestralized mission lands, contributing to the Guaraní War of 1754–1756. Sepé Tiaraju, associated with São Miguel, became a celebrated resistance leader before his death. Iberian forces defeated the Guaraní, and the mission was depopulated and damaged. The treaty was later annulled, but recovery remained fragile; Jesuit expulsion from Spanish territories in 1767 removed the order's administration.

São Miguel continued under secular and other religious authorities, then suffered further conflict, looting, and abandonment as borders shifted. Vegetation and weather reduced roofs and domestic buildings, leaving the great church walls as the dominant ruin. Brazilian preservation began in the early twentieth century. National heritage authorities listed the site in 1938, stabilized the masonry, and created the Missions Museum, designed by Lúcio Costa, to shelter religious sculptures gathered from the region. Conservation practices have evolved toward greater archaeological restraint and Indigenous participation.

UNESCO inscribed São Miguel in 1983 and linked it with four mission ruins in Argentina in 1984 as the Jesuit Missions of the Guaranis. The site is both a monument of colonial evangelization and a place within living Guaraní memory. Present interpretation increasingly resists portraying the missions solely as a European achievement or vanished utopia. The ruined church, plaza, museum, and surrounding community speak to artistic collaboration, coercion, refuge, Indigenous agency, imperial border-making, war, abandonment, and the continuing struggle over who defines this heritage. Continuing Guaraní engagement also challenges the older museum language that treated Indigenous life as ending when the reduction became a ruin.