The monastery was founded by king García Sánchez III “the one from Nájera” and his wife Doña Estafanía de Foix who commissioned its construction in 1052. The origin of its foundation are misted in the legend which tells how the king was out hunting and chased his prey into a cave where he found a mysterious image of the Virgin and a jar of lilies, a bell and a lantern. Some time later the king reconquered the Lower Rioja city of Calahorra from the Moors and built the monastery of Santa María La Real as an offering to the Virgin for her help.
In 1079 Alfonso VI of Castile incorporated the monastery into the Benedictine order of Cluny together with the group of clergy who lived in it from its creation and who remained until the disendowment of Mendizábal in 1835. Since 1895 a community of Franciscan friars have run the monastery