Mutagenesis breeding via ethyl methanesulfonate (EMS) has been successfully used in faba bean to improve some economically important traits. However, there is a knowledge gap of the factors/mechanisms related to its sensitivity/tolerance to EMS treatment toxicity. It was hypothesized that the seed size could influence the response of the diverse botanical varieties of faba bean. Consequently, we conducted a comprehensive assessment of the sensitivity of six faba bean varieties: three major varieties (Aguadulce superlonga, Reina mora, and Yasmine) and three minor varieties (Zina, Alfia 05, and Alfia 17), to three increasing concentrations (0.05%, 0.5%, and 1%, along with a control 0%) of EMS. Analyses included various germination parameters (germination percentage [GP], germination energy at seven and 14 days [GE7 and GE14], germination rate index [GRI], and vigor index [VI]) across different EMS concentrations. To further explore mechanisms involved in sensitivity to EMS, we measured coat thickness and assessed antioxidant activity. Our findings revealed that the seed size variation did not significantly affect EMS sensitivity. Different varieties showed significant responses to increasing EMS concentrations (p ≤ 0.05) for most parameters, except for root length. This challenges the assumption that the seed size influences EMS sensitivity in faba bean. Coat thickness was uniform, suggesting similar EMS absorption. DPPH assay revealed significant antioxidant activity differences between nontreated and EMS‐treated groups. Antioxidant activity correlated significantly with germination parameters under EMS treatment. The study indicates factors beyond seed size contribute to EMS responses. Examining antioxidant systems may explain plants’ ability to counteract EMS‐induced oxidative stress.