This study aimed to (1) examine the cross-sectional area (CSA) of the masseter muscle in relation to bruxism and (2) investigate if there are gender-related differences in the masseter muscle in a population-based magnetic resonance imaging (MRI) study. The study included 720 subjects aged 30-89 years (391 women and 329 men) from the Study of Health in Pomerania, a cross-sectional population-based study assessing the prevalence and incidence of common population-relevant diseases and their risk factors in Northeastern Germany. The participants underwent both a whole-body MRI and a full oral examination. The CSAs of the masseter muscles on both sides were measured from MRI images. The presence or absence of awake and/or sleep grinding and clenching, unilateral chewing, and other parafunctional activities were obtained from the dental interview. Linear and ordinal logistic regression models were used to examine the associations between the CSAs of the masseter, bruxism, and gender. The frequency of bruxism and reports of muscle or joint pain were significantly higher in women. The analysis revealed that a larger masseter CSA was significantly associated with bruxism only in men. The larger CSA was manifested only in the higher frequency bruxers. Bruxism had heterogeneous effects on the masseter muscle between genders. Although a higher prevalence of bruxism was reported by women, the larger CSA of the masseter muscle was significantly higher in bruxing men but not in women. This study emphasizes the need for a gender-specific approach when evaluating the clinical implications of bruxism on the masseter muscle.