The “Caliphal City of Medina Azahara” was built in 936–937 CE or 940–941 CE (depending on the source) by the first Caliph of al-Andalus Abd al-Rahman III, being recently inscribed (2018) on the UNESCO World Heritage List. The abandonment and destruction of the city have been traditionally related to the civil war (“fitna”) that started between 1009 and 1010 CE. However, we cannot rule out other causes for the rapid depopulation and plundering of the city just a few decades after its foundation. The archaeoseismological study provides the first clues on the possible role played by an earthquake in the sudden abandonment and ruin of the city. Eleven different types of Earthquake Archaeological Effects (EAEs) have been identified, such as dropped key stones in arches, tilted walls, conjugated fractures in brick-made walls, conjugated fractures and folds in regular pavements and dipping broken corners in columns, among others. Besides that, 163 structural measures on EAEs were surveyed resulting in a mean ground movement direction of N140°–160° E. This geological structural analysis clearly indicates a building-oriented damage, which can be reasonably attributed to an earthquake that devastated Medina Azahara during the 11st or 12th centuries CE. If this were the case, two strong earthquakes (≥VIII MSK/EMS) occurred in 1024–1025 CE and 1169–1170 CE could be the suspected causative events of the damage and destruction of the city.