The occurrence of two Alternaria mycotoxins, alternariol (AOH) and alternariol monomethyl ether (AME) and the presence of conidia from Alternaria spp., were investigated throughout the food production chain of two businesses, one which uses organic fruit and the other non-organic. For this purpose, a propidium monoazide (PMA) treatment followed by a quantitative Real Time PCR (qPCR) was used to detect and quantify viable conidia exclusively. Results demonstrated that 68.4% of the total raw fruit analysed was contaminated with viable Alternaria spp. Regarding the mycotoxin occurrence, only a few samples were contaminated with AME, while 35% of raw tomatoes tested positive for AOH in the organic producer and 21% in the non-organic producer. AOH was present in samples analysed before heat treatment, while almost no mycotoxins were found in the final products of the organic producer. However, in the non-organic producer, 47% of the tomato concentrates were contaminated.