The building is one of the earliest Spanish examples of Gothic architecture, built at a time when the Romanesque style still predominated in the Iberian Peninsula.

The facade was partially reconstructed in the neo-Gothic style in 1910 to repair damage caused when the bell tower (the Giraldo) collapsed in 1902 after being struck by a lightning.

[2] On 21 September 1177, Alfonso VIII of Castile, "The Noble", defeated the Moors after a nine-month siege and conquered the city of Cuenca.

Characteristic of the Romanesque style, there were initially five staggered apses, a single transept and three naves in the main body of the building.

In the 17th century, the cathedral chapter retained architect Ventura Rodríguez to build the altar of Saint Julian, also known as el Transparente for the stained glass illuminating and decorating the background of the altarpiece.

The iconography of Cuenca Cathedral is largely fantastical, with mythological and human figures interspersed amongst plant leaves, stems, fruits and meandering streams.

[9] From readings of the Book of Revelation and the "Centuries" in Les Propheties by Nostradamus, the scholar and architect Rodrigo de Luz concluded that the Holy Grail was saved and preserved in this cathedral.

[10] It has been claimed that there are other hidden messages in the iconography of the cathedral and of the City of Cuenca, including a coat of arms featuring a cup with an octagram or eight-pointed star, symbol of the Knights Templar.