This study presents a comparative analysis of two risk assessment methodologies applied to the processing of whole oranges with edible coatings, a novel approach aimed at extending shelf life and enhancing food safety. The research addresses a critical gap in food safety management, where the selection of risk matrices for hazard evaluation often lacks standardized guidance, leading to variability and subjectivity in decision-making. Using a case study from a mid-sized agro-industrial company in Spain, hazards were systematically identified across processing stages, including physical, chemical, and microbiological risks. Two assessment tools were applied: a 4 × 4 qualitative risk matrix based on probability and severity, and the Failure Mode and Effects Analysis (FMEA) method, which integrates severity, likelihood of occurrence, and likelihood of detection. Results from both approaches identified the same significant hazards and determined equivalent Critical Control Points (CCPs) and stricter Prerequisite Programs (PRPs), including key stages such as fungicide treatment, disinfection, rinsing, sorting, and coating preparation. However, the FMEA method provided additional insights into the detection capability of existing control measures, offering a more comprehensive framework for Hazard Analysis and Critical Control Points (HACCP) validation. These findings demonstrate that both tools are suitable for assessing risks in edible-coated orange processing, but the FMEA method is recommended for its enhanced ability to evaluate the effectiveness of detection systems. The study contributes to harmonizing risk assessment practices and supports the fruit industry in implementing robust, evidence-based food safety strategies.