In Tunisia, apiculture represents a growing strategic sector. In fact, honey production increased from 220 tons in 1970 to 2500 tons in 2020. However, this sector still suffers, as worldwide, from a lack of traceability and a risk of fraud which can impact honey quality. To guarantee food safety, farmers and food processors need to base their efforts on risk analysis.  Failure mode and effect analysis (FEMA) is a safety and reliable analysis tool: it allows the identification of failures that could happen on a system and provides their effects and consequences. Conducting risk analysis during honey production would reduce incidents, contribute to risk management associated with the honey human consumption, save costs and improve competitiveness in the market. This research was conducted within a large scale honey production unit (1500 modern beehives) in Nabeul governorate (north-east of Tunisia). FMEA model was applied in conjunction with cause-and-effect analysis for the risk assessment of honey production. Potential failure modes and effects as well as their possible causes were identified in the honey process flow. Criticality of each failure was calculated taking into account risk, frequency and gravity. Qualitative diagnosis during honey process flow revealed 56% of nonconformities, based mainly on failures of implementation of good hygiene and good farming practices. Moreover, highest criticality was attributed to the presence of humid honey frames, honey rehumidification, microbiological contamination, fermentation and ineffectiveness of cleaning. Based on the FMEA analysis, an improvement plan for all stages was suggested with an emphasis on rising employees’ awareness and training.