Pathogenic microorganisms can grow accidentally on fish origin human food and can be a cause of human food‐borne illness. The purpose of this study was to estimate the occurrence and microbial load pattern of Escherichia coli , Salmonella , Staphylococcus aureus , and Shigella spp. along the fish origin food value chain. A total of 396 fish samples were collected by a systematic random sampling technique of cooked and raw in the three species of fish. Fish muscles were tested using selective media, followed by conventional biochemical tests. The bacterial load was assessed using a standard plate count method. Whereas the fungal load were measured by cultured in a Sabouraud's dextrose agar (SDA) medium. The overall prevalence was Escherichia coli 84 (21.21%), Salmonella 27 (6.82%), Staphylococcus aureus 19 (4.80%), and Shigella spp. 17 (4.29%). The average mean total coliform count was observed 1.2 × 10 2 cfu/g and 5.10 × 10 4 cfu/g in cooked and raw fish samples, respectively. Whereas total viable count mean of 8.05 × 10 4 cfu/g and 11.5 × 10 4 cfu/g in cooked and raw fish, respectively. The Fungal load counts under the range 5.6 × 10 1 cfu/g to 1.09 × 10 3 cfu/g were observed. The study has revealed that fish food in the study area has the possibility of microbial public health risk. Hence, it could be wise to improve the knowledge of key actors from harvesting to consumption to enhance the meals protection practices and high‐quality standards of fish foods.