Due to the large number of complaints from some cheese producers in the El-Beheira Governorate, Egypt about the existence of problems in their cheese products, it was important to identify the causes of these problems and to provide recommendations and practical solutions. The Hazard Analysis and Critical Control Points (HACCP) system is a plant-specific and product-specific quality system that is one of the most significant systems in quality assurance and food safety programs. As a result, the application of the HACCP system plan in a small-scale cheese plant producing fresh damietta and ras cheese was investigated in order to determine the effect of the HACCP system application on microbiological hazards by determining the bacterial load of Critical Control Points (CCPs). The obtained results revealed that raw milk and equipment swabs were the most dangerous sources of contamination with different microorganisms. In addition, that the diversity of microorganisms and their counts in some raw materials, food handlers and food contact surfaces, besides, the processing conditions have an impact on the quality and safety of the product. The most prevalent fungal isolates from production line of both cheese factories were Rhodotorula followed by Candida spp, regarding to mould species penicillium and Asp. niger were the most prevalent mould species. Therefore, all instructions for implementing the HACCP system were prepared, including a flow diagram of processing processes, identifying risks, regulating at different CCPs by monitoring and corrective actions, confirming the HACCP plan, and keeping records.