Innovative engineering design for biologically active hydroxyapatites requires enhancing both mechanical and physical properties, along with biocompatibility, by doping with appropriate chemical elements. Herein, the purpose of this investigation was to evaluate and elucidate the model of naturally occurring hydroxyapatite and the effects of doped trace elements on the function of normal human fibroblasts, representing the main cells of connective tissues. The substrates applied (geological apatites with hexagonal prismatic crystal habit originated from Slyudyanka, Lake Baikal, Russia (GAp) and from Imilchil, The Atlas Mountains, Morocco (YAp)) were prepared from mineral natural apatite with a chemical composition consistent with the building blocks of enamel and enriched with a significant F− content. Materials in the form of powders, extracts and single-crystal plates have been investigated. Moreover, the effects on the function of fibroblasts cultured on the analyzed surfaces in the form of changes in metabolic activity, proliferation and cell morphology were evaluated. Apatite plates were also evaluated for cytotoxicity and immune cell activation capacity. The results suggest that a moderate amount of F− has a positive effect on cell proliferation, whereas an inhibitory effect was attributed to the Cl− concentration. It was found that for (100) GAp plate, fibroblast proliferation was significantly increased, whereas for (001) YAp plate, it was significantly reduced, with no cytotoxic effect and no immune response from macrophages exposed to these materials. The study of the interaction of fibroblasts with apatite crystal surfaces provides a characterization relevant to medical applications and may contribute to the design of biomaterials suitable for medical applications and the evaluation of their bioavailability.