In the fermentation of Monascus, in addition to the production of various beneficial active substances, such as monacolin K and Monascus pigments, citrinin is also produced, resulting in renal toxicity. Therefore, its wide application is restricted. Exploring safe and reliable methods to reduce citrinin in Monascus products is of great significance to further expand their application range. This study investigated the effect of genistein on the production of the fungal toxin, citrinin, and pigments by solid fermentation of the filamentous fungus Monascus aurantiacus Li AS3.4384, which is widely used in food and medicine. With the addition of 2.0 g/L genistein, citrinin production decreased by approximately 50%, while pigment production increased by 23%. With addition of 2.0 g/L genistein dissolved in dimethyl sulfoxide, citrinin production decreased by 96.2%, and pigment production decreased by 26.3%. With the addition of 2.0 g/L genistein and 0.06 g/L baicalein, citrinin production decreased by 87.9%, and pigment production decreased by 35.5%. Therefore, the synergistic effect of genistein and baicalein may provide a new method to reduce Monascus citrinin production in industry.