In a papal bull from 1199 where Privileges were granted to the monasteries of San Millán de la Cogolla it appears with the name Coculla, which comes from the Latin word cuculla, small hill, hilltop; this word is typically used for high sites and those of defensive nature, coming from the times of the Reconquista.

The monastery and the surrounding area suffered in the civil war between Peter of Castile and Henry II of Castile which involved a major confrontation nearby, the Battle of Nájera (April 1371).

Those affected included the small Jewish community (aljama) of San Millán.

In 1369 Henry II of Castile made an order in their favour, "the Christian men and women and the Moorish men and women" should immediately discharge all their debts to the Jews, "that the last-named might be able to pay their taxes the more promptly."

On September 10, 1371, however, the king released the abbot and all the monks of San Millán from whatever debts they had contracted with the Jews since the Battle of Nájera.