A challenging task in analytical chemistry is an application of renewable and natural materials for isolation of hazardous substances such as antimicrobial drugs from environmental samples. The energy-efficient scalable hydrothermal procedure to fabricate the eco-friendly “switchable” sorbent based on hydroxyapatite nanoparticles with in situ modified surface using a small amount of capping agents was developed. Sorbents characterization including the surface composition investigation via quantum-chemical calculation based on the original approach was provided. The sorbents demonstrated well expressed controllable surface switching and high values of the sorption and elution efficiency for tetracycline, oxytetracycline, and chlortetracycline achieved by simple change of the medium pH. These processes were thoroughly discussed based on the results of chemical and computational experiments. A simple and universal strategy for choosing a suitable sorbent for solid phase extraction of target analytes was proposed for the first time. It was shown that the developed eco-friendly sample preparation procedure with use of biocompatible sorbents could be applied both for removal of target analytes from sample matrix (water samples) as well as for the quantitative analytes determination after elution step. It is believed that the presented research is significant for the determination of different amphoteric analytes in wide variety of samples.