According to the scientific information reviewed, cheese is highly susceptible to contamination by mycotoxin-producing fungi, primarily species from the genera Aspergillus (A. niger, A. flavus) and Penicillium (P. commune, P. solitum, P. palitans, and P. crustosum). Studies on various types of cheese made from cow’s milk report an average concentration of Aflatoxin M1 (AFM₁) at 13,000 ng kg⁻¹, which is alarming since the regulatory limits for AFM₁ in cheese range from 250 to 500 ng kg⁻¹. For instance, limits set by Codex Alimentarius, the European Commission (EC), Turkey, and Iran are 250 ng kg⁻¹. In the Netherlands, the limit is 200 ng kg⁻¹, and in Italy, it is 450 ng kg⁻¹. However, the concentration of mycotoxins frequently exceeds these regulatory limits, including critical mycotoxins such as ochratoxin A, citrinin, and cyclopiazonic acid, which pose significant global health concerns. Therefore, this study aims to review the mycobiota responsible for producing key mycotoxins in cheese and to assess the influence of physicochemical factors on fungal growth and mycotoxin production. By incorporating control strategies such as hygiene practices, pasteurization, and the use of preservatives, this study seeks to improve methodologies in the cheese production chain and mitigate contamination by fungi and mycotoxins.