Discs of biocompatible glass ionomer cements were prepared for Hertzian indentation and subsequent fracture analyses. Specifically, 2 × 10 mm samples for reproducing bottom-initiated radial fracture, complemented by 0.2 × 1 mm samples for optimal resolution with X-ray micro tomography (μCT), maintaining dimensional ratio. The latter allowed for accurate determination of volumetric-porosity of the fully cured material, fracture-branching through three Cartesian axes and incomplete bottom-initiated cracking. Nanocomputed tomography analyses supported the reliability of the μCT results. Complementary 2-dimensional fractographic investigation was carried out by optical and scanning electron microscopies on the larger samples, identifying fracture characteristics. The combined 3-D qualitative assessment of microstructure and fractures, complemented by 2-D methods, provided an increased understanding of the mechanism of mechanical failure in these cements. Specifically, cracks grew to link pores while propagating along glass-matrix interfaces. The methodological development herein is exploitable on related biomaterials and represents a new tool for the rational characterisation, optimisation and design of novel materials for clinical service.