The aim of this study was to compare the nutritional and use value of berries grown in organic and conventional systems. The polyphenol content, fruit colour and firmness, and yeast, mould, and mycotoxin contents were assessed in blueberry fruit freshly harvested and stored for 8 weeks in controlled conditions (CA: CO2-12%; O2-1.5%, temperature 1.5 °C). The Shannon-Wiener diversity index was comparable in both systems and was lower for mould in organic fruit than in conventional fruit. Mycotoxins (deoxynivalenol, zearalenone) were found only in organic fruits. The optimal mineral content and pH of the soil allowed the cultivation of blueberry in accordance with organic standards. The storage of highbush blueberry fruit in CA cold storage for 8 weeks resulted in a slight deterioration in fruit quality and polyphenol content. The lower nutritional value of these fruits is compensated by the lack of pesticides and artificial fertilizers residues. The use of fungicides in conventional cultivation reduces the population of sensitive fungi and therefore reduces the contamination of fruits with mycotoxins.