This research documents and graphically analyzes the pavilions muqarnas at the Court of the Lions in the Alhambra in Granada, a World Heritage Site. In order to cast some light on the understanding and preservation of these 14th century architectural elements, after a brief report of historical data on catastrophes and restorations, a novel methodology for the case study based on three complementary graphic analyses is presented here: First, there is a review of outstanding images ranging from the 17th to the 20th centuries; subsequently, new CAD (computer-aided design) drawings from pavilions muqarnas testing the theoretic principles from their geometric grouping are accomplished for the first time; and finally, a 3D laser scanner is used to understand the precise present-day state from the point cloud obtained. Comparing drawings allows us to assess the muqarnas relevance while proving, for the first time, that the muqarnas of both pavilions have distinct configurations and different amounts of pieces. Besides, this process reveals geometric deformations existing in the original Nasrid muqarnas compositions, identifying small pieces hitherto unknown, plus additional deformations resulting from adjustments after important threats that both pavilions and their muqarnas overcame for centuries, despite their fragile construction.