Background/Objectives: Emotional eating is a behavioral pattern in which individuals increase food intake in response to emotional states rather than physiological hunger. University students are particularly vulnerable due to academic stress, lifestyle changes, and a food environment dominated by highly palatable options. Although emotional eating has been associated with adiposity and metabolic alterations, evidence in Mexican university populations remains limited. This study aimed to estimate the prevalence of emotional eating and to examine its association with anthropometric and biochemical indicators in students from the Universidad Autónoma de Querétaro (UAQ). Methods: A cross-sectional study was conducted among 670 first-year university students participating in the SU SALUD-UAQ clinical evaluation. Emotional eating was assessed using the 10-item Emotional Eater Questionnaire (EEQ). Anthropometric measures (body mass index BMI, body fat percentage, and waist circumference) and biochemical markers (triglycerides, total cholesterol, HDL cholesterol, and glucose) were obtained through standardized clinical procedures. Associations were evaluated using multivariable linear and logistic regression models adjusted for sex, age, physical activity level, sleep duration, stress, and socioeconomic status. Results: The prevalence of emotional eating categories was as follows: non-emotional (33.5%), low emotional (31.1%), emotional (27.6%), and highly emotional (7.8%). Higher EEQ scores were independently associated with greater BMI, body fat percentage, and waist circumference in both sexes. In women, emotional eating was also independently associated with less favorable lipid profiles. In addition, students classified as emotional or highly emotional eaters showed higher odds of general and abdominal obesity, particularly among women. Conclusions: Emotional eating is highly prevalent among Mexican university students and is independently associated with increased adiposity in both sexes and with altered lipid profiles in women. These findings highlight the relevance of integrating emotional regulation strategies into university health programs as a component of comprehensive health promotion approaches aimed at addressing emotional eating and its associated anthropometric and metabolic correlates in young adults.