In this study, magnesium (Mg), zinc (Zn), and strontium (Sr) incorporated amorphous calcium carbonate (ACC) nanoparticles were synthesized. Results revealed that at low Zn concentrations, Zn and Sr co-incorporated, Mg-stabilized amorphous calcium carbonate (ACMC) nanoparticles were obtained. However, at high Zn concentrations, instead of ACMC, calcium (Ca) and Sr co-incorporated, magnesium-stabilized amorphous zinc carbonate (AZMC) nanoparticles were obtained. Our results demonstrated that Mg could be used to stabilize the amorphous structure of both nanoparticles. The additive ions could be incorporated into the structure of both ACMC and AZMC without impairing their amorphous nature. The synthesized nanoparticles had an average size of about ∼30 nm. Degradation studies suggested that the degradation rate of AZMC nanoparticles could be slower compared to ACMC nanoparticles. Antibacterial tests showed that the number of colony forming units for the Ca and Sr co-incorporated AZMC nanoparticles was lower for both Staphylococcus aureus (S. aureus), and Escherichia coli (E. coli) strains compared to the control group. Cytotoxicity studies revealed that fibroblasts interacting with the ion-incorporated ACMC and AZMC nanoparticles remained viable and proliferated for up to 5 days in vitro. These results demonstrated for the first time that Zn and Sr co-incorporated ACMC nanoparticles were non-toxic, biodegradable, and possessed antibacterial properties. In addition, Ca and Sr co-incorporated AZMC nanoparticles exhibited a stronger antibacterial effect, which makes them promising candidates for antibacterial applications.