The official procedure adopted in Andalusia (Southern Spain) for implementing the hazard analysis and critical control points (HACCP) flexibility criteria for the control of the cold chain in the retail self-service sector set out in Regulation (CE) 852/2004 is based on a daily determination of the display temperature of the equipment. The main objective of our study was to test whether this approach was effective for the safety of the storage products, considering the influence of the position occupied by the foodstuffs inside the cooling equipment, and also possible seasonal fluctuations. The study was conducted in all self-service refrigerating equipments from every food retail store (11 supermarkets representing different national chain-store groups) located in various municipalities from Southern Spain. Statistically significant (p ≤ 0.05) breaches in the cold chain were recorded in the case of products located at the top shelf (TST) for all kinds of foodstuffs during the summer period, and also during winter time in the cases of TST of dairy products and refrigerated vegetables. Furthermore, using predictive microbiology as a tool, we calculated the potential reduction caused by those failures on the shelf life recorded in the food labelling of smoked salmon, cooked chicken breast and fresh cheese, which counted up to 40%, 57% and 25%, respectively. These findings show that the official procedure adopted does not ensure compliance with safety specifications of perishable food in the retail self-service sector. A revision of such procedure would be necessary, especially in those regions such as Andalusia where important temperature fluctuations throughout the year are recorded.