Essential oils are natural antimicrobial agents that can be used to control fungal and mycotoxin contamination. Although there are numerous reports discussing the fungal and mycotoxin contamination of foods, there are few researches on baby food contamination so this work aimed to determine the fungal and mycotoxin contamination in cerelac, cornflakes and milk powder and tried to control the mycotoxigenic strain growth and their production of mycotoxins by using essential oils. Cornflakes were heavily contaminated (24 species including 9 genera), while cerelac and milk powder were less contaminated. Aspergillus and Penicillium were the prevalent genera. The produced aflatoxins and ochratoxins from the tested strains of Aspergillus flavus and A. niger were extracted and estimated by fluorometric method. We used the 18S rRNA sequence technique to identify the genotypes of the three isolates. Two isolates were identified as Aspergillus niger and the third isolate as A. flavus. Omt‐A gene was detected in the A. flavus, while Aopks gene was detected in A. niger isolates. Amongst the five used essential oils, only cumin and peppermint oil depressed the mycotoxigenic strain growth and peppermint oil had the highest result. Its inhibitory effect on aflatoxin and ochratoxin production was evaluated. Aflatoxin production was highly reduced by 52.1%, but ochratoxin inhibition was very low, 4.88% and 3.17% by A. niger obtained from cornflakes and milk powder, respectively. The three tested samples were contaminated by ochratoxins, but cerelac and milk powder samples were free of aflatoxins. Cornflakes sample recorded the highest reading for both toxins.