Background: The Allium cepa test is a widely used, cost-effective, and versatile model for assessing cytogenotoxicity. Cytotoxicity is determined through changes in root growth and the mitotic index, while genotoxicity is identified through chromosomal aberrations such as breaks, bridges, and micronuclei. Objective: To synthesize the methodological principles, applications, and interpretation of the assay’s endpoints, with emphasis on environmental monitoring, nanotoxicology, and the evaluation of emerging materials. Methods: An exploratory analytical approach was applied to identify and compare studies employing the Allium cepa assay across different contexts. The literature, selected from scientific databases, was organized to highlight methodological diversity and biomarker performance. Conclusions: Compared with other models, Allium cepa stands out for its simplicity, the availability of multiple cytogenotoxic markers, and its minimal ethical constraints, making it especially suitable for research in low-infrastructure settings. Future studies should work toward the international standardization of methodologies, the integration of this model with molecular and omics-based approaches, and its incorporation into predictive frameworks for environmental and human health risk assessment. In an increasingly complex toxicological landscape, Allium cepa emerges as a pivotal tool for enhancing toxicological surveillance and safeguarding biological systems.