Background As a result of increased demand for environmental and health-conscious cosmetics, retailers have increasingly marketed their products using terms such as “clean” or "non-toxic". Sephora, a popular beauty retailer, implemented a clean seal system to label and promote their products. This study aims to compare the toxicity concerns of clean vs. non-clean products by using the Environmental Working Group (EWG)'s Skin Deep framework. Methods EWG’s Skin Deep Framework was used to rank products based on their cancer, allergy and immunotoxicity, developmental and reproductive toxicity, and use-restriction concerns, with lower scores indicating a cleaner product (ranging 0–10). The distributions of EWG scores among clean and non-clean products were investigated and stratified by different types of products (i.e. fragrance, hair, makeup, or skincare). A multivariable linear regression model was further applied to evaluate the association between EWG scores and clean seals, adjusting by types of products, level of toxicity concerns. Results 356 products were screened, including 180 (50.56%) clean products and 176 (49.44%) non-clean products. Clean products yielded a higher percentage of low hazard ingredients compared to non-clean products. EWG scores are positively correlated with the levels of toxicity concern for cancer, allergy and immunotoxicity, respectively. Clean products are also associated with a lower EWG score by 0.71 in the regression model. Fragrance products are most hazardous, with a 2.42 increase in EWG score. Conclusions Products under the binary “clean beauty” labeling system at Sephora may not necessarily capture the nuances of EWG’s ten-point scoring system and various dimensions of health concerns. It may be insufficient for consumers to solely rely on the presence of the clean seal when purchasing beauty products. Consulting multiple frameworks and sources to inform decision-making is crucial in addressing knowledge gaps. Further research and increased data availability from EWG’s database are necessary as well as public education on the application of Sephora’s clean seal.