Originally, the entire interior of the building was a large hypostyle hall used as a prayer hall, with the sole exception of the rooms in the double wall of the quibla. Apart from its religious use, which included the five daily prayers and the special Friday prayer, the hall was also used as an educational and Shari'a centre during the rule of Abderraman I and his successors.

The hall was large and flat and was covered with wooden ceilings supported by a double arcade resting on columns. These arches divided the foundational mosque into eleven naves from north to south, later enlarged by Almanzor to nineteen naves. Approximately 850 columns were made of jasper, onyx, marble, granite and porphyry. In the foundational mosque, all the columns and capitals were reused from Roman and Visigothic buildings, although subsequent extensions, beginning with Abderraman II, incorporated new Islamic capitals evolving from the Roman ones. The nave leading to the mihrab, which was the central nave until Almanzor ended its symmetry, is slightly wider than the rest, demonstrating a subtle hierarchy in the mosque's design. The double arcade was an innovation that allowed for a higher ceiling, consisting of a horseshoe arch in the lower part and a semi-circular arch in the upper part. The famous red and white voussoirs of the arches were inspired by the Dome of the Rock95 and are also reminiscent of Aachen Cathedral, which were built almost contemporaneously. The horseshoe arch was already known in the Iberian Peninsula from the Visigothic period, for example it was used in the church of San Juan de Baños, and to a lesser extent in Byzantine and Umayyad regions of the Middle East; however, the Islamic horseshoe arch evolved with its own, more characteristic and sophisticated version. The mosque's architectural system of the double arch is considered one of the most innovative features and has been the subject of many opinions. The hypostyle hall has been described as a 'forest of columns' and has a similar effect to a 'hall of mirrors'.

The original ceiling of the mosque was made of wooden planks and decoratively carved and painted beams. Original fragments have been preserved, some of which are displayed in the courtyard of the Orange Trees, which were discovered in the 19th century and have enabled modern restorers to reconstruct the ceiling in some of the western sections of the mosque in its original style. In contrast, the eastern aisles, which belong to the Almanzor extension, are now covered with semi-circular vaults made in the 17th century, with the exception of the southern section, which is covered with Gothic vaults made by Hernán Ruiz first in the 16th century. On the outside there are gabled roofs covered with tiles.