Yogurt is the most popular dairy product in Egypt. The popularity of yogurt can be attributed to its sensory characteristics and nutritional value. The microbiological characteristics of yogurt also contribute greatly to the quality and shelf life of the final product. One hundred yogurt samples were collected from local market stores and were examined for their culture viability of lactic acid bacteria (Lactobacillus spp. and Streptococcus spp.), Bacillus spp., psychrophilic bacteria (Pseudomonas spp.), pathogenic bacteria (Salmonella spp., Staphylococcus spp. and Escherichia coli) and some common fungi (Aspergillus spp. and Penicillium spp.) before and after chilled conditions for 10 days at 7ºC ±1. Yogurt culture population maintained a high population (7-9 log CFU/ml) after chilled storage condition with increasing the probability to prevent foodborne illness in consumers. Here, the psychrophilic bacteria ranged from 5-6 log CFU/ml, whereas the other tested groups ranged from 2-4 log CFU/ml. Storage condition period decreased the number of pathogenic bacteria which showed statistically significant level as comparing after and before storage. Our research demonstrates the importance of implementation of HACCP technique as a quality control practices to ensure the highest yogurt quality in Giza, Egypt. In addition, we report bacterial identification using MALDI-TOF MS as simple, effective, time and cost-effective technique which can be used in a different application instead of the conventional method that were cumbersome and cost-consuming.