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While it has long been mimicked by simple precipitation reactions under biologically relevant conditions, calcium phosphate biomineralization is a complex process, which is highly regulated by physicochemical factors and involves a variety of proteins and other biomolecules. Alkaline phosphatase (ALP), in particular, is a conductor of sorts, directly regulating the amount of orthophosphate ions available for mineralization. Herein, we explore enzyme-assisted mineralization in the homogeneous phase as a method for biomimetic mineralization and focus on how relevant ionic substitution types affect the obtained minerals. For this purpose, mineralization is performed over a range of enzyme substrate concentrations and fluoride concentrations at physiologically relevant conditions (pH 7.4, T = 37 °C). Refinement of X-ray diffraction data is used to study the crystallographic unit cell parameters for evidence of ionic substitution in the lattice, and infrared (IR) spectroscopy and X-ray photoelectron spectroscopy (XPS) are used for complementary information regarding the chemical composition of the minerals. The results show the formation of substituted hydroxyapatite (HAP) after 48 h mineralization in all conditions. Interestingly, an expansion of the crystalline unit cell with an increasing concentration of the enzyme substrate is observed, with only slight changes in the particle morphology. On the contrary, by increasing the amount of fluoride, while keeping the enzyme substrate concentration unchanged, a contraction of the crystalline unit cell and the formation of elongated, well-crystallized rods are observed. Complementary IR and XPS data indicate that these trends are explained by the incorporation of substituted ions, namely CO32− and F−, in the HAP lattice at different positions.