BackgroundAntibiotics, which are the most important medication in human history, have brought global concerns due to their potential risk to human health and environment by accelerating the development of drug-resistant bacteria, and accumulating in the food chain system. Among antibiotics, oxytetracycline (OTC) is widely used in aquaculture, and its potential risk of toxicity to human by bioaccumulation has been reported. Therefore, the effective removal of OTC is highly needed.ResultsIn this study, we report bio-hybrid inorganic microparticles (apt-mag-SiCC) for efficient capturing and facile magnet-based separation of oxytetracycline (OTC). These bio-hybrid inorganic microparticles are composed of magnetic separable silica coated calcium carbonate microparticles (mag-SiCC) derived from CO2, conjugated with oxytetracycline binding aptamers (OBA). These bio-hybrid inorganic microparticles were successfully synthesized, based on the characterization data obtained by SEM, FT-IR, EDAX, BET, and CLSM. About 6 μm sized bio-hybrid inorganic microparticles showed low non-specific adsorption to OTC and other molecules, and the selective capturing towards to the OTC in both buffer and tap water. Moreover, these bio-hybrid mineral microparticles were found to be stable, even after the repeated usages, maintaining the initial capturing efficiency.ConclusionUsing the newly synthesized bio-hybrid inorganic microparticles, we could successfully capture OTC by facile magnet-based separation. With advantages of theses bio-hybrid inorganic microparticles such as easy fabrication, low-price, and environmental friendliness, this novel material could be utilized in the drinking water treatment, in vitro medicinal diagnostics, or in vitro removal of antibiotics lining out from the blood (blood purification).Electronic supplementary materialThe online version of this article (10.1186/s13036-018-0113-8) contains supplementary material, which is available to authorized users.