Microcystins (MCs) are a family of cyanotoxins and pose detrimental effects on human, animal, and ecological health. Conventional water treatment processes have limited success in removing MCs without producing harmful byproducts. Therefore, there is an urgent need for cost-effective and environmentally-friendly methods for treating MCs. The objective of this study was to develop sustainable and non-chemical-based methods for controlling MCs, such as using cold plasma and ultra violet (UV) light with titanium dioxide (TiO2) coating, which can be applied for diverse scale and settings. MCs, extracted from Microcystis aeruginosa, were treated with cold plasma or UV at irradiance of 1470 μW/cm2 (high) or 180 μW/cm2 (low). To assess synergistic effects, the outside of the UV treatment chamber was coated with nanoparticles (TiO2) prior to irradiation, which can be reused for a long time. The degradation efficiency of UV was enhanced by the reusable TiO2 coating at lower irradiance (70.41% [UV] vs. 79.61% [UV+TiO2], 120 min), but no significant difference was observed at higher irradiance. Cold plasma removed MCs rapidly under experimental conditions (92%, 120 min), indicating that it is a promising candidate for controlling MCs in water without generating harmful disinfection byproducts. It can be also easily and practically used in household settings during emergency situations.