Background: Aflatoxin M1 (AFM1) is hepatotoxic and carcinogenic, and it may be present in milk due to dairy cow's ingestion when feed is contaminated with Aflatoxin B1 (AFB1). Aim: The objective of this research was to determine the potential risk factors of dietary AFB1 contamination in dairy cows, which causes AFM1 contamination of the raw milk, through an epidemiological survey and statistical analysis. Methods: 209 raw milk samples were collected, and AFM1 concentrations were detected by lateral flow immunochromatographic assay. Results: It was determined that 100% of the samples contained concerning levels of this mycotoxin with a mean of 0.077 μg/kg, which exceeds the maximum allowed by the European Union legislations (0.05 μg/kg) but not Ecuadorian Regulations (0.5 μg/kg). An adjustment to a linear model by weighted least squares was used to correct the presented heteroscedasticity. Potential risk factors for dietary AFB1 contamination were analyzed in relation to the appearance of AFM1 in milk from Ecuador. Among factors including legumes consumption, the use of silage, type of production system (intensive, extensive, and mixed), and farm size (small, medium, and big), the intensive production system and the big producers presented higher levels of AFM1. Conclusion: Considering that all the milk samples presented AFM1 and since there is no specific feed determined to be a risk factor, it was concluded that any of the feed offered to dairy cows may be contaminated with AFB1. It is necessary to reduce AFB1 levels in feed by implementing good agricultural practices and improving feed storage to decrease milk AFM1 levels. This study identified that intensive systems have a lot of animals, and silage is incorporated into the diet, which can significantly increase AFM1 levels.