Good manufacturing practices play an important role in obtaining safe food and preventing foodborne diseases. To achieve this goal, food handlers must receive appropriate training to be aware of their responsibilities. In this work, compliance with specific personal hygiene requirements by food handlers was assessed in a cross-sectional study of traditional small retail establishments, namely butcher (n = 56) and fishmonger (n = 17) shops in Almada, Portugal. Food handlers (n = 140, of which 113 worked in butcher shops, and 27 worked in fishmonger shops) were interviewed for data collection, and retail establishments were audited considering specific hygiene requisites. In fishmonger shops, most food handlers are women (89%), aged 18 to 45 years (70%), with a high school degree, having worked for less than 5 years in this activity, while in butcher shops most food handlers are men (90%) over 45 years old (58%), with a basic education level, and more than 26 years of experience. Most food handlers (>95%) attended recent food safety and hygiene training courses and were able to recognize that hand sanitizers cannot replace a proper hand wash, and to identify Staphylococcus aureus transmission routes to food. However, approximately 23% of retail establishments failed to provide hot water in the handwashing basin and exhibited improper placement of handwashing instructions. Furthermore, these establishments did not implement corrective actions following non-conforming microbiological results of hand hygiene monitoring. These findings reinforce the need for consistent management commitment, and for providing food handlers with regular training, which is crucial for maintaining a strong food safety and hygiene culture in these traditional small retail establishments.