The use of yeast to biologically control the production of ochratoxin A, which is caused by filamentous fungal growth, in coffee farms is a promising alternative to conventional methods. However, yeast strains, environmental field conditions, and the chemical composition of grains / fruits can influence the effectiveness of biological control agents. We tested the efficiency of different yeast strains in controlling three species of ochratoxigenic fungi in a coffee-based medium. The reasons and mechanisms behind the varying sensitivities of different Aspergillus species to biological control remains unclear. Aspergillus carbonarius rapidly assimilated carbon sources, giving it an advantage over yeasts in substrate colonisation. Saccharomyces cerevisiae CCMA 0159 inhibited all three fungal species, achieving efficiencies of 74.4%, 100%, and 80.9% against A. carbonarius, A. westerdijkiae, and A. ochraceus, respectively. The strategies employed by S. cerevisiae CCMA 0159 to inhibit the growth of ochratoxigenic fungi included competition, production of fungicidal volatile compounds, and alteration of the substrate's physicochemical properties. Our results indicate that among the yeast isolates tested, S. cerevisiae CCMA 0159 is the most effective in inhibiting ochratoxigenic fungi in coffee, including the more resistant A. carbonarius.