Suso is the older building and is believed to be built on the site of a hermitage where Saint Emilian (Spanish: San Millán) lived.

The scriptorium produced the second phase of the San Millán Beatus and remained active during the period of Muslim rule; and over the centuries, the religious community has overcome various vicissitudes which affected the monasteries (for example being sacked by the Black Prince).

However the type of monastic life evolved: the original monks living at Suso were hermits, but Yuso, the refoundation of the monastery on a lower site, developed as a Benedictine community.

As the UNESCO evaluation noted, San Millán shows the transformation from an eremitic to a cenobitic community in material terms.

San Millán attracts pilgrims on the Way of St James (even though it lies somewhat off the line of the official route between Nájera and Burgos).