Onion peel waste was tested to explore its anti-cyanobacterial activity on the growth of Microcystis aeruginosa. First, the onion peel was extracted by maceration using three different solvents: aqueous water, ethanol, and ethyl acetate. The efficacy of the aqueous, ethanol, and ethyl acetate extracts of onion peel against M. aeruginosa was assessed using both microdilution and paper disc diffusion techniques. Secondly, in a batch bioassay, the anti-cyanobacterial effect of the ethyl acetate extract, as the most active extract, on M. aeruginosa growth and pigment production was evaluated. To identify the potential allelochemicals, total phenolic and total flavonoid contents were analyzed in the different extracts. The obtained results demonstrated the ability of the ethyl acetate extract of onion peel to inhibit M. aeruginosa growth. This effect was dose-dependent. The highest inhibitory rate (99%) was achieved on day 8 under the highest concentration (100 mg/L). Consequently, all treatment groups exhibited a significant reduction in chlorophyll-a and carotenoid contents compared to the control group. The preliminary results demonstrated the anti-cyanobacterial effect of the ethyl acetate extract of onion peel on Microcystis growth and suggest it as a potential eco-friendly solution for controlling Microcystis blooms in eutrophic water bodies.