Today, given the paramount importance of food safety to human health, mycotoxins are considered especially important contaminants of foodstuffs. Among the mycotoxins, aflatoxins are potent food contaminants which are present in maize and wheat. Invasions of toxigenic fungi in the field and during storage are directly affected by climate and other environmental factors. A total of 129 samples of maize and grain harvested in 2022 were surveyed for mycological contamination. Aflatoxin B1 contamination was investigated using the enzyme-linked immunosorbent assay (ELISA) method.Our study revealed the presence of fungi from five genera: Aspergillus, Fusarium, Penicillium, Alternaria, and Cladosporium. We also found that maize was more frequently contaminated than wheat. Fungi of the Penicillium genus were the most abundant (77.89%), followed by Fusarium (74.73%) and Aspergillus (72.63%). Samples originating from the Korça region (104 units) exhibited a higher fungal load on the three genera. AFB1 contamination is a more critical issue in maize than wheat. The incidence of AFB1 in maize was 88.23%, with a maximum concentration of 69.12 μg/kg; in contrast, the incidence of AFB1 in wheat was only 4.91%. In wheat, no samples had AFB1 concentrations above the EU Maximum Residue Level (MRL) of 2 μg/kg; in maize, 41.18% of samples exceeded the AFB1 MRL of 5 μg/kg for human food, and 32.25% exceeded the MRL for animal feed. These findings, together with other research results from the last decade, suggest that relevant information should be made available to farmers, and good agriculture practices encouraged, as a matter of priority.