Supermarket food sales data might serve as a simple indicator of population-level dietary habits that influence the prevalence of excess weight in local environments. To test this possibility, we investigated how variation in store-level food sales composition across Switzerland is associated with the mean Body Mass Index (BMI) of young men (Swiss Army conscripts) living near the stores. We obtained data on annual food sales (2011) for 553 stores from the largest supermarket chain in Switzerland, identified foods commonly regarded as “healthy” or “unhealthy” based on nutrient content, and determined their contribution to each store’s total sales (Swiss francs). We found that the sales percentages of both “healthy” and “unhealthy” food types varied by 2- to 3-fold among stores. Their balance ranged from −15.3% to 18.0% of total sales; it was positively associated with area-based socioeconomic position (r = 0.63) and negatively associated with the mean BMI of young men in the area (r = −0.42). Thus, even though we compared supermarkets from a single chain, different shopping behaviors of customers caused stores in privileged areas to sell relatively more healthy food. Knowledge about such patterns could help in designing in-store interventions for healthier nutrition and monitoring their effects over time.