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The fabrication of bioactive three-dimensional (3D) hydrogel scaffolds from biocompatible materials with a complex inner structure (mesoporous and macroporous) and highly interconnected porosity is crucial for bone tissue engineering (BTE). 3D-printing technology combined with aerogel processing allows the fabrication of functional nanostructured scaffolds from polysaccharides for BTE with personalized geometry, porosity and composition. However, these aerogels are usually fragile, with fast biodegradation rates in biological aqueous fluids, and they lack the sterility required for clinical practice. In this work, reinforced alginate-hydroxyapatite (HA) aerogel scaffolds for BTE applications were obtained by a dual strategy that combines extrusion-based 3D-printing and supercritical CO2 gel drying with an extra crosslinking step. Gel ageing in CaCl2 solutions and glutaraldehyde (GA) chemical crosslinking of aerogels were performed as intermediate and post-processing reinforcement strategies to achieve highly crosslinked aerogel scaffolds. Nitrogen adsorption–desorption (BET) and SEM analyses were performed to assess the textural parameters of the resulting alginate-HA aerogel scaffolds. The biological evaluation of the aerogel scaffolds was performed regarding cell viability, hemolytic activity and bioactivity for BTE. The impact of scCO2-based post-sterilization treatment on scaffold properties was also assessed. The obtained aerogels were dual porous, bio- and hemocompatible, as well as endowed with high bioactivity that is dependent on the HA content. This work is a step forward towards the optimization of the physicochemical performance of advanced biomaterials and their sterilization.