The present study describes the implementation of a food safety system in the dairy pilot plant “Gourmeticus Academicum,” a spin-off within the University of Agricultural Sciences and Veterinary Medicine of Cluj Napoca, Romania. In order to improve Hazard Analysis of Critical Control Points (HACCP) the preliminary programs were integrated into the quality management system (QMS) by monitoring the biological hazards. The process provides future specialists with good practice hands-on and educational tools. This study focused on hazard analysis, the determination and establishment of prerequisite programs, and the role of critical control points (CCPs) based on HACCP and the challenges found during the process as a critical thinking model on education programs. The determination of the CCPs in the processing of yogurt was made by applying the decision tree method. Besides, biological hazards are included as a by-control of the system’s implementation performance. For the successful implementation of HACCP principles, prerequisite programs (PRPs) and operational prerequisite programs (OPRPs) were initially implemented. This process could be challenging but feasible to be reached in small-scale food industries with remarkable results as educational tools.