Egusi pudding is one of the most popular traditional dishes of the Cameroonian population. Besides its nutritional values, it is also endowed with a sociocultural character. Nowadays, consumer demand for Egusi pudding has increased and the dish is sold as street food in several cities of Cameroon and mostly under uncontrolled hygienic conditions. The objective of this study was to assess the microbiological quality of Egusi pudding sold in the city of Yaoundé taking into consideration the protein sources and the sampling sites. Five types of Egusi pudding samples based on protein sources were randomly collected from 25 sellers distributed in 7 districts in the city of Yaoundé and their microbiological quality were assessed. The results showed that the total aerobic count of the different samples (2.97 ± 0.03 to 4.43 ± 0.05 Log CFU/g) was under the threshold value (5.47 Log CFU/g) recommended for food intended for human consumption. Loads of fecal coliforms (1.47 ± 0.00 to 5.47 ± 0.00 Log CFU/g) in 40% of samples, Escherichia coli (2.39 ± 0.12 to 5.43 ± 0.05 Log CFU/g) in 60% of samples, fecal streptococci (2.90 ± 0.15 to 4.74 ± 0.05 Log CFU/g) in 88% of samples, Pseudomonas spp. (3.39 ± 0.15 to 5.43 ± 0.06 Log CFU/g) in 100% of samples, and the presence of Salmonella spp. in 56% of samples revealed a poor level of hygiene of the vendors. Pathogens associated with unsafe food handling such as Staphylococcus spp. were found in 100% of samples at loads (3.84 ± 0.18 to 5.43 ± 0.05 Log cfu/g) higher than the norms of the European Commission. Potential toxigenic pathogens such as Clostridium perfringens, Yersinia enterocolitica, Bacillus cereus, and moulds were also found, respectively, in 100, 96, 96, and 100% of samples. Overall, the most contaminated samples were those made with sardine as protein source, 92.85% (n = 23/25), followed with beef (88.57%), mackerel (84.28%), cod (82.85%), and control (77.1%). The results of this study suggest that important measures should be taken by the Public Health Service in order to sensitize the producers and vendors of Egusi pudding on the respect of good hygiene, manufacturing practices, and the continuous monitor of the quality of traditional products sold in markets.