The aim of this work was to determine the influence of substituted hydroxyapatites heat treatment on the citrate sorption behavior. Hydroxyapatites doped with sodium and magnesium ions were obtained and subjected to heat treatment at the temperature range of 80–600 °C. All the minerals were characterized in detail with the use of infrared spectroscopy. Next, the adsorption of citrate ions was conducted on the apatites at the solid-solution interface. For each mineral, its maximum monolayer capacity was determined. For the initial hydroxyapatites (80 °C), the characterization using energy dispersive X-ray microanalysis and the study of citrate adsorption kinetics were also performed. Additionally, the thermodynamic adsorption parameters were calculated. The studies showed that both doping as well as heat treatment have indirect influence on the adsorption capacity of hydroxyapatites with regard to citrates. The highest adsorption capacity was observed for the hydroxyapatite doped with magnesium ions and subjected to heat treatment at 80 °C. The conclusions from this study could be of importance for the process of producing composite materials containing hydroxyapatites.