The primary intention of present study was to determine the incidence of microbial load & some pathogens in filled bakery products available in bakeries & supermarkets. A total number of 122 samples (65 chicken sandwiched burger and 57 butter cream pastries) were microbiologically analyzed. By using the standard microbiological techniques like spread plate method, pour plate method & streak plate method to examined the microbial count in these products. Further isolation & identification of microbes was performed by using selective microbiological media & bacterial biochemical identification kits. Among the chicken sandwiched burgers 75.38% of the samples had reasonable and satisfactory microbiological quality with appropriate aerobic plate count and absence of tested pathogenic microorganisms. But 4 samples were found to be potentially hazardous due to the presence of Salmonella and Staphylococcus aureus in three & one samples respectively. Whereas 64.91% sample of the buttered cream pastries were of good microbiological quality. 12.28% butter cream pastry samples were classed as unsatisfactory due to high aerobic plate count, high coliform count and presence of the fungal contaminants. Overall 62.29% of the sampled filled baked products were of satisfactory quality while only 3.27% samples had poor microbiological quality including those which were potentially hazardous to the health of the consumer. To save consumer health & spoilage of the products good hygienic practices & HACCP system should be implemented during production of filled bakery products.