Scaffolds which aim to provide an optimised environment to regenerate bone tissue require a balance between mechanical properties and architecture known to be conducive to enable tissue regeneration, such as a high porosity and a suitable pore size. Using freeze-dried collagen-based scaffolds as an analogue of native ECM, we sought to improve the mechanical properties by incorporating hydroxyapatite (HA) in different ways while maintaining a pore architecture sufficient to allow cell infiltration, vascularisation and effective bone regeneration. Specifically we sought to elucidate the effect of different hydroxyapatite incorporation methods on the mechanical, morphological, and cellular response of the resultant collagen-HA scaffolds. The results demonstrated that incorporating either micron-sized (CHA scaffolds) or nano-sized HA particles (CnHA scaffolds) prior to freeze-drying resulted in moderate increases in stiffness (2.2-fold and 6.2-fold, respectively, vs. collagen-glycosaminoglycan scaffolds, P < 0.05, a scaffold known to support osteogenesis), while enabling good cell attachment, and moderate mesenchymal stem cell (MSC)-mediated calcium production after 28 days' culture (2.1-fold, P < 0.05, and 1.3-fold, respectively, vs. CG scaffolds). However, coating of collagen scaffolds with a hydroxyapatite precipitate after freeze-drying (CpHA scaffolds) has been shown to be a highly effective method to increase the compressive modulus (26-fold vs. CG controls, P < 0.001) of scaffolds while maintaining a high porosity (˜ 98%). The coating of the ligand-dense collagen structure results in a lower cell attachment level (P < 0.05), although it supported greater cell-mediated calcium production (P < 0.0001) compared with other scaffold variants after 28 days' culture. The comparatively good mechanical properties of these high porosity scaffolds is obtained partially through highly crosslinking the scaffolds with both a physical (DHT) and chemical (EDAC) crosslinking treatment. Control of scaffold microstructure was examined via alterations in freezing temperature. It was found that the addition of HA prior to freeze-drying generally reduced the pore size and so the CpHA scaffold fabrication method offered increased control over the resulting scaffolds microstructure. These findings will help guide future design considerations for composite biomaterials and demonstrate that the method of HA incorporation can have profound effects on the resulting scaffold structural and biological response.