Metformin (MET), an antidiabetic compound, has received increasing attention, as it cannot be effectively removed during conventional wastewater treatment processes and may act as an endocrine disruptor. Electron beam irradiation (EBI) is an eco-friendly process able to degrade and neutralize biohazardous pollution almost instantly. In this context, this study applied EBI to MET degradation and detoxification in aqueous solutions. A 98% MET degradation rate and TOC removal of 19.04 ± 1.20% at a 1.0 kGy EBI dose was obtained, with up to 65% mineralization reached at 5.0 kGy. Toxicity assays were performed with Vibrio fischeri, Saccharomyces cerevisiae, and Daphnia similis, and the findings indicate that generated byproducts were only more toxic to D. similis. This reveals the need to assess organisms belonging to different trophic levels. A cytotoxic assessment employing Allium cepa roots demonstrated no toxic effects concerning untreated and irradiated samples.