Analyses of ergosterol (ERG), adenosine-5?-triphosphate (ATP) and groups A and B trichothecenes were performed in three Triticum monococcum cultivars registered in Germany (Albini, Terzino and Tifi), grown in the organic system. The experiment was carried out on two dates: the first - in the final phase of flowering (BBCH 69) and the second - in the phase of full ripeness (BBCH 89). The analyses were performed on shanks, glumes, grain and awns. Concentrations of analyzed metabolites in different parts of T. monococcum plants varied significantly. Mean ERG concentration in the first term was more than 30 times higher than immediately before harvest, whereas for group B trichothecenes it was 4 times higher. Contents of ATP and concentrations of group A trichothecenes were similar at both times. When analyzing parts of the spike, the highest amount of metabolites was recorded in shanks (ERG - 114 mg/kg, ATP 900,000 RLU, group A and B trichothecenes - 0.07 and 0.20 mg/kg, respectively), while the lowest in grain (ERG - 5 mg/kg, ATP 55,000 RLU, group A and B trichothecenes - 0.03 and 0.08 mg/kg, respectively). A higher ERG concentration was found in awns (65 mg/kg) than in glumes (41 mg/kg), whereas for ATP and group A and B trichothecenes by contrast higher concentrations were recorded in glumes (160,000 RLU, 0.06 and 0.029 mg/kg, respectively) than in awns (77,000 RLU, 0.05 and 0.014 mg/kg, respectively). Recorded results indicate a potential occurrence of trichothecenes in shanks, awns and glumes already during flowering, when grain has not yet developed. In these parts of plants, after harvest, the highest amounts of microorganisms and Fusarium toxins were found, which pose a threat for farmers and workers employed in the cereal industry.