The consumption of organic produced food has steadily increased over the last decade, which stands out to be better-tasting, safer and ecologically friendly. A few differences in vitamin- and mineral levels are reported between organic and conventional food, but no health-benefits of consuming organic food have yet been proven. This study was aimed at investigating whether organic and conventional wheat flour differed in fungal profile and levels since a limited use of pesticides in organic production occurs. The amount of fungi was calculated as cfu/g of wheat flour and fungal identification was performed with a MALDI-TOF Biotyper. Interestingly, no significant difference was found between organic and conventional wheat flour. However, we faced contradictory results between different brands since one brand showed higher microbial levels in conventional wheat flour while the organic flour had higher levels in a different brand. Remarkably, mycotoxin-producing fungus Aspergillus clavatus was detected in one of the organic wheat flour. Therefore, further research is needed to investigate the effectiveness of prevention methods of fungi and where in the organic food production system the mycotoxin-producing fungal species develops.