Plastic pollution in aquatic ecosystems has become a significant problem especially microplastics which can encapsulate into the skeletons of organisms that produce calcium carbonates, such as foraminifera, molluscs and corals. The encapsulation of microplastics into precipitated aragonite, which in nature builds the coral skeleton, has not yet been studied. It is also not known how the dissolved organic matter, to which microplastics are constantly exposed in aquatic ecosystems, affects the encapsulation of microplastics into aragonite and how such microplastics affect the mechanical properties of aragonite. We performed aragonite precipitation experiments in artificial seawater in the presence of polystyrene (PS) and polyethylene (PE) microspheres, untreated and treated with humic acid (HA). The results showed that the efficiency of encapsulating PE and PE-HA microspheres in aragonite was higher than that for PS and PS-HA microspheres. The mechanical properties of resulting aragonite changed after the encapsulation of microplastic particles. A decrease in the hardness and indentation modulus of the aragonite samples was observed, and the most substantial effect occurred in the case of PE-HA microspheres encapsulation. These findings raise concerns about possible changes in the mechanical properties of the exoskeleton and endoskeleton of calcifying marine organisms such as corals and molluscs due to the incorporation of pristine microplastics and microplastics exposed to dissolved organic matter.