Introduction: Fish, including Oreochromis shiranus (Chambo), is a vital protein source in Malawi, but consumption has declined. Due to its perishability, preservation methods like smoking and frying are common. This study compares microbial load in smoked and fried tilapia from wholesale and retail markets. Materials and methods: This cross-sectional study compared the microbial load in smoked and fried tilapia (Chambo) from wholesale (Salima) and retail (Lilongwe) markets. Twenty fish samples (10 smoked, 10 fried) were collected, transported in sterile conditions, and analyzed for Total Aerobic Plate Count and coliforms using ISO-standard methods. Data were log-transformed and analyzed using two-way ANOVA, with significance set at p < 0.05. Results: Fried tilapia from wholesalers had low levels of contamination, with most samples showing too few colonies to count (TFTC), while some smoked samples displayed higher bacterial counts (33.75±3.77 CFU/mL). Retailer samples showed a wider range of bacterial species, including Escherichia coli and Pseudomonas putida, suggesting potential hygiene concerns. Overall, bacterial loads were significantly higher in tilapia from retail markets compared to those from wholesalers (p < 0.05). Conclusion: The analysis showed higher microbial contamination in tilapia from retailers, with greater bacterial diversity, including E. coli, indicating poor hygiene. Wholesaler samples had minimal contamination. Although preservation methods showed no significant difference in microbial loads, retailer fish had significantly higher bacterial loads