The inlet became the original port of Santander in the Middle Ages. The evidence points to the existence of a 9th century abbey, the origin not only of the cathedral but of the whole city itself. The present cathedral was begun in the latter third of the 12th century, when the Fuero was granted to Santander; the lower section, the church of El Cristo, was started first, with the construction of the Cathedral beginning immediately after and continuing through the first third of the 13th century until the final completion of the cathedral cloister.

Thus in the late 13th century and early 14th the "High" or "Old" Town of the city of Santander stretched, in the manner of other medieval cities, in linear fashion, along a low ridge that cut into the bay in an east-west direction. At the end of this promontory stood the two most significant buildings: the collegiate church and the castle of San Felipe.

During the late Middle Ages the town spread northwards, where the "Low" or "New" Town sprang on the opposite bank of Becedo stream, as Braun's engraving shows. The rising class of merchants and innkeepers settled here, linked to the town's commercial development and differing markedly from the fishermen and seafarers who lived in the Old Town.