The Royal Monastery of San Millán de Yuso is located in the town of San Millán de la Cogolla, on the left bank of the Cárdenas River, in the heart of the San Millán Valley.

It is part of the monumental complex of two monasteries, together with the oldest Monastery of San Millán de Suso.

This monastery was ordered to be built in 1053 by King García Sánchez III of Navarra.

The history of its foundation is linked to a legend based on a miracle of Saint Millán, a young shepherd who becomes a hermit. When Millán died in 574, at the age of 101, his disciples buried him in his cave, and around it the first monastery was formed, that of San Millán de Suso. Saint Braulio, fifty years after Saint Millán's death, writes his life.

Navarrese King García III was very devoted to San Millán. As he had just founded the great monastery of Santa María la Real de Nájera in this city that was the court of the kingdom, he wanted to take the mortal remains of the saint there, which were buried in the monastery of San Millán de Suso.

On May 29, 1053, they placed the remains of the Saint in a cart drawn by oxen and thus began the journey, to the great discontent of the monks who were left devastated by the loss of their patron. When they reached the plain, near the river, the oxen stopped and did not want to walk again; there was no way to force them. The king and the entire entourage understood that this was a miracle, that San Millán was imposing his will not to go from there and be buried again in those places. It was then that the king ordered the construction of the recent monastery, which was called Yuso, in contrast to the one above Suso.

Until at least the year 1100, the two monasteries coexisted, the one above, Suso, and the one below, Yuso. The first remains faithful to tradition: Mozarabic rule and a dual male and female community character. The second, reformed with the Benedictine rule.