In view of expanding cultivation of cereal mixtures, the study was conducted to examine the effects of organic (ORG) vs conventional (CON) farming on fungal contamination, concentrations of phenolic acids (PA) and metals in mixtures of cereals grown in northern and central regions of Poland. The analyses were performed on 10 ORG and 8 CON bulk samples of oat, wheat and barley mixtures, each one comprised samples taken from 4 – 5 farms. Fungal contamination was assessed as the concentration of ergosterol (ERG) and mycotoxins from trichothecene (TR) group, whereas the quantification of fungal species and TR genotypes was performed using TaqMan assay. Mean ERG content in grain produced in both systems was similar, although a markedly greater variation was recorded in ORG grain. Total TR mycotoxins concentration was, in both CON and ORG samples, low and comparable, however concentration of deoxynivalenol was considerably greater whereas that of 3-acetyl-deoxynivalenol (3-AcDON) and 15-AcDON and nivalenol were lower in ORG samples. Molecular analysis showed that the dominant fungi were Fusarium culmorum and F. graminearum. The Tri5 gene, a precursor of TR formation, was detected in significantly greater relative amounts in ORG samples. The ORG cereal mixtures contained greater total amounts of PA and, in particular, of gallic, p-cumaric and ferulic acids. Concentrations of Cd, Cu and Mg did not differ between the ORG and CON cereals, whereas concentrations of Fe, Se and Zn were greater in CON, and those of Mn and Pb in ORG mixtures. The potentially hazardous substances were present in the samples of both CON and ORG cereal mixtures in concentrations which do not compromise the health of farm animals.