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Maize is considered a staple crop in Guatemala and is consumed in high amounts in the rural areas of the country. Given that traditional pre- and post-harvest practices lead to environmental exposure to pests and microorganisms, maize quality and safety can be compromised severely. In order to assess the potential degree of risk, maize from six farms from Huehuetenango, Guatemala were evaluated based on their mycobiota. For all of the farms, moisture levels during storage remained above 14% increasing the possibility of fungal colonization. Fungal load was estimated using DRBC agar. Moreover, DNA was extracted from the maize samples, and ITS1F-TW13 amplicons were subjected to Illumina sequencing. Overall, fungal counts from harvest and throughout storage were constant at approximately 5 log CFU/g. For the farms where the maize moisture content exceeded 20%, a high yeast content was observed which can reflect spoilage during storage. Findings showed a significant amount of <i>Fusarium</i>, a mycotoxin-producing mold, which could lead to mycotoxin contamination. This indicates a potential for compromising the health of the inhabitants of the region where maize represents a significant portion of the diet. Moreover, fungal endophytes <i>Stenocarpella maydis</i> and <i>Acremonium sp</i>. were also found in significant amounts across farms, indicating damage of the maize plant. Insect damage is another indicator of risk as it may result not only in entry points for fungi but can also act as vectors for such microorganisms. An entomological analysis revealed an overall incidence of <i>Ephestia kuehniella</i> (flour moth) of 32%, <i>Sitophilus zeamais</i> (maize weevil) of 16% and <i>Tribolium sp</i>. (flour beetle) of 8% for the analyzed farms. Results from this study can help better understand the current health-risk scenario in the Highlands of Guatemala incurred by performing poor grain handling practices.