The effective elastic modulus of composite materials results from a combination of elastic moduli of the component phases. Recent efforts to understand the mechanical behavior of calcified tissues in bones and teeth require estimates of the component phase properties, which are difficult to establish independently. A three-phase system, based on naturally occurring bone, is therefore examined by a combined nanoindentation and finite element modelling approach to better understand the proportions and properties of the component phases. Bone samples were prepared in four two- or three-phase composite configurations as follows: (1) as a dehydrated mineral-protein composite (with some void space); (2) similarly dehydrated mineral-protein composite but with polymethylmethacrylate (PMMA) resin filling the voids resulting in three solid phases; (3) as a PMMA-mineral composite following protein removal and replacement with PMMA, and (4) as a PMMA-protein composite following mineral removal and replacement with PMMA. Effective component volume fractions and elastic moduli for each phase in each system were computed based on the composite nanoindentation results. Finite element models of the two- and three-phase systems were constructed to explore the structural anisotropy of the composite systems, as demonstrated in the nanoindentation tests, and to examine the sensitivity of the composite results to changes in the assumed component properties.