The aim of this study was to evaluate the concentration of aflatoxin M1 (AFM1) in milk from Holstein-Friesian cows on local farms located in two different cities in Turkey, to investigate the effect of this mycotoxin on milk quality and seasonal variation, and to investigate the efficacy of a commercial clay-based binder. As part of the study, milk samples from 144 dairy cows were analyzed for the presence of AFM1 prior to the use of a clay-based toxin binder. As a result of this analysis, 26.9% of milk samples from individual animals had AFM1 levels exceeding the U.S. permissible limit of 0.5 µg/kg. In addition, AFM1 was detected in 36.5% of winter and 18.6% of summer milk samples. The presence of AFM1 caused a decrease in milk fat, dry matter, and protein levels. The affected animals were further divided into two groups: control group (n = 14) and experimental group (n = 26). The animals of the experimental group were fed 25 g/animal of clay-based binder toxin daily. The treatment group showed a gradual decrease in AFM1 levels by 24.4% on day 4 and 48.9% on day 7. In addition, the fat, non-fat solids, and protein content of milk increased significantly. As a result, a high level of AFM1 contamination in milk was detected, which can be assumed to negatively affect the quality of milk production. The use of clay-based toxin binders may be an effective method to improve milk quality and protect animal and consumer health.