Fungal infections in cereals lead to huge economic losses in the food and agriculture industries. This study was designed to investigate the occurrence of toxigenic fungi and their mycotoxins in marketed cereals and explore the effect of the antagonistic yeast Cyberlindnera jadinii volatiles against key toxigenic fungal strains. Aspergillus spp. were the most frequent contaminating fungi in the cereals, with an isolation frequency (Fr) of 100% in maize, followed by wheat (88.23%), rice (78.57%) and oats (14.28%). Morphological and molecular identification confirmed the presence of key toxigenic fungal strains in cereal samples, including A. carbonarius, A. flavus, A. niger, A. ochraceus and A. parasiticus. Aflatoxins (AFs) were detected in all types of tested cereal samples, with a significantly higher level in maize compared to wheat, rice, oats and breakfast cereals. Ochratoxin A (OTA) was only detected in wheat, rice and maize samples. Levels of mycotoxins in cereals were within EU permissible limits. The volatiles of Cyberlindnera jadinii significantly inhibited the growth of A. parasiticus, A. niger and P. verrucosum. The findings of this study confirm the presence of toxigenic fungi and mycotoxins in cereals within the EU permissible limits and the significant biocontrol ability of Cyberlindnera jadinii against these toxigenic fungi.