Contamination of food chains by toxigenic fungi and aflatoxins is a global problem that causes damage to human health, as well as to crop and livestock production. The objective is to evaluate Aspergillus flavus and total aflatoxins (AFs) occurrence in totally mixed rations (TMRs) for dairy cows and aflatoxin M1 (AFM1) in milk for human consumption. Ninety-nine dairy production units located in Aguascalientes, Mexico, were randomly selected, and samples were collected from TMRs, raw milk, and milk marketed in the city in two consecutive agricultural cycles. AFs were quantified in TMRs and milk by indirect enzyme immunoassay and HPLC; aflatoxigenic and molecular (PCR) capacity of monosporic A. flavus isolates in the feed was characterized. All feed, raw, and pasteurized milk samples showed aflatoxin contamination (26.0 ± 0.4 µg/kg, 32.0 ± 1.0, and 31.3 ± 0.7 ng/L, respectively), and a significant proportion (90.4, 11.3, and 10.3%) exceeded the locally applied maximum permissible limits for feed and milk (20.0 µg/kg and 50 ng/L). Aflatoxin contamination in both TMRs and milk indicated a seasonal influence, with a higher concentration in the autumn–winter cycle when conditions of higher humidity prevail. The results obtained suggest the existence of contamination by aflatoxigenic A. flavus and aflatoxins in the diet formulated for feeding dairy cows and, consequently, in the dairy food chain of this region of the Mexican Highland Plateau.