The present study aimed to assess the performance of food safety management systems in food retail stores via audits to reveal potential areas of improvement and to find out possible corrective actions to suggest to the top management. Two cycles of on-site audits took place in 106 stores to assess the requirements and hygiene conditions. After the first cycle of audits, improvements were suggested to the top management, and a second cycle of audits took place after a reasonable time. In the checklist, we recorded the temperatures of retail refrigerators and the scores from the inspection of hygiene and HACCP documentation. In the A′ audit, the percentage of stores that had higher temperatures than the critical limits was equal to 51%, and those temperatures occurred in the refrigerators for salads, followed by the refrigerators for deli meat, yogurts and desserts. In the B′ audit, only the refrigerators for salads exhibited percentages that were statistically significant lower (p-value < 0.05), and the stores were improved after the audit. High percentages of high-scoring stores were observed in the A′ and B′ audit in the inspection of HACCP documentation, although there was not a statistically significant improvement observed (p-value > 0.05). In the hygiene inspection, statistically significant improvement with 95% confidence appeared for “Refrigerator’s products appearance”, “Storage cleanliness”, and “Grocery shelf cleanliness”. The highest number of non-conformities without statistically significant improvement was found for “Checking temperatures of the receiving products” and “Labeling of fruit store products”, with the percentages being lower than 15% in both of the audit cycles. Many employees of the stores did not check and record the temperatures of receiving products from suppliers. In addition, the storage of spoiled products beneath fresh products for selling in the same refrigerator is not a good practice. Greater efforts must be made by top management and employees to maintain and distribute food products in the best and safest possible hygiene conditions.