Objective This study aims to characterise the occupational exposure to the bioburden of groceries workers and to identify the most critical workstations. Background To our knowledge, this is the first study performed in Portugal that intends to characterise the microbial contamination in this specific setting. Method This study was conducted between November and December of 2020 in fifteen groceries stores (M) located in the municipality of Cascais. Passive sampling methods (Electrostatic dust cloths—EDC) and surface swabs were used at three different locations (checkout, fruits/vegetable and warehouse/dispenser areas). EDC and surface swabs were inoculated in four standard culture media, namely, malt extract agar (MEA), dichloran glycerol (DG18), tryptic soy agar (TSA) and violet red bile agar (VRBA) for further characterisation. Results The prevalence of bacterial contamination was higher than fungal contamination in both sampling methods. The highest prevalence was in the fruits/vegetable area regarding fungal and bacterial contamination. Conclusion The sampling methods employed effectively identified the most critical workplaces regarding microbial contamination. Application This study will be useful for industrial hygienists since it is the first held in small grocery shops focusing in the occupational exposure assessment of microbiological contamination.