Aflatoxin contamination and rancidity in locally processed commercial fish feeds and ingredients along value chains is a Public and Animal health hazard. The study established the level of aflatoxin contamination, peroxide value (PV), Anisidine value (AnV), and their associated factors at storage areas among farmers, processors, traders, factories, and landing sites in the Wakiso and Kampala districts. The value chain actors were purposively selected in a cross-sectional study based on access to the feed store and the use of locally processed commercial fish feeds on farms. Data collected were statistically analyzed in SPSS version 20. All the samples (45) were positive for aflatoxin contamination and PV with 51% (23/45) of samples being contaminated with “above acceptable” aflatoxin levels and 66.6% (30/45) of samples with “above acceptable” PV. The overall percentage of “above acceptable” AnV was 11/29 (37.9%). Samples from factories were within acceptable contamination levels. Multivariate logistic regression analysis revealed no significant difference between aflatoxin contamination, peroxide, and Anisidine value with storage factors for locally processed commercial fish feeds and ingredients. The study recommended the purchase of fish feeds from factories and a larger study on storage factors responsible for aflatoxin contamination and rancidity in fish feeds in Uganda.