The work is devoted to obtaining calcium-phosphate (Ca/P) coatings based on hydroxyapatite using the RF magnetron sputtering method and conducting SEM, TEM, and X-ray structural analysis. It was established that the power of the RF discharge, the bias voltage on the substrate, the working gas atmosphere, and the sputtering time determine the Ca/P ratio in the coating and its structure. Controlling the basic parameters of sputtering, changing the coating structure from amorphous to crystalline components, and improving the ratio of the main elements are possible. The morphology of the formed coatings was studied, and the average grain size was measured. For all types of coatings, rectilinear and curvilinear crystal boundaries were found, which correspond to arbitrary orientations of neighboring blocks. A common feature was the formation of a nano-sized subgranular structure within each columnar crystallite with extinction contours, demonstrating the coating material’s highly stressed state. Calcium-phosphate coatings on oxidized and non-oxidized samples of stainless steel and titanium obtained by RF magnetron sputtering of hydroxyapatite targets in various gas environments were characterized by high nanohardness (8.4–11.9 GPa) and elastic recovery (41–52%), which is a favorable factor for implants working under load.