Several samples of ancient mortars were studied in the context of the archaeological excavations at Djehuty (Luxor, Egypt). The studied mortars had two different applications: to render external walls and as structural elements (adobe walls, contact between stone blocks, etc). An understanding of the mechanical stability of these materials is necessary in order to guarantee correct preservation of the remains. However, their mechanical characterisation using standard tests would require large samples (over 50 mm in cubic/cylinder form), which archaeological excavations are unlikely to be able to provide. The aim of this research was to analyse the mechanical behaviour of different gypsum mortars by means of the uniaxial micro-compression test and relate this to their microstructure. The microstructure is described in terms of the mineralogical composition (XRD), texture (SEM) and pore structure (MIP). Results showed that the studied gypsum mortars presented a very low strength and elastic modulus (0.25-1.60 MPa and 97.56-260.97 MPa, respectively). These mechanical characteristics are closely related to the mortar microstructure, since they presented a highly porous texture (57.93-68.35%), a polymodal pore size distribution in the 0.1-10 m range, and low contact between crystals (very open texture). Micro-compression characterisation of ancient mortars and building rocks was compared to meso-compression results found in the literature and confirmed the effectiveness of the micro-compression test as a low-invasive technique for characterising materials from architectural heritage.