[2] Archeological vestiges from the Roman epoch are found in the north of the village until the margins of the River Ardila, but they suggest the fields of Amaraleja were occupied by various generations during the pre-history of the region.

[3] Roman remnants include the pavements of buildings, circular burial tombs with bowls and fragments of bone, coins with the inscriptions of Emperor Claudius, roof tile, masonry and milling stones.

[3] During the reign of Sancho II, the municipal seat of Moura was conquered from the Moors, and a feudal seigneurial system was imposed in the region.

Amareleja was a victim of Spanish pillaging during the Restoration Wars; 300 mounted soldiers entered the village and sacked the homes, left, and returned later to re-sack the populace, which put up no resistance.

[3] A map from the 18th century, identifying the Alentejo campaigns during this period, shows the encounters between Spanish and Portuguese forces in Marilla (Amarelas) and Pedras, which were places near Amareleja.

Following these events, the Portuguese archbishopric petitioned Pope Benedict XIV to invoke Saint Francisco de Borja in Portugal's post disaster reconstruction, promising processions throughout the cities and towns in the Kingdom, on the second Sunday in November.

Like the rest of Alentejo and Ribatejo, Amareleja is very prone to heat waves in the summer months and has recorded one of the highest temperatures ever in Europe at 47.4 °C (117.3 °F).