The present study examined the influence of primary food components on the antifungal activity of the essential oil of Origanum vulgare, carvacrol, thymol, eugenol, and trans-cinnamaldehyde against Penicillium verrucosum and Aspergillus westerdijkiae. The MIC was determined in food model media enriched with proteins (1, 5, or 10%), carbohydrates (1, 4, or 6%), or oil (1, 5, or 10%). Proteins increased the antifungal activity of O. vulgare essential oil, carvacrol, thymol, and eugenol, whereas the effect of trans-cinnamaldehyde decreased with increasing protein content. The presence of carbohydrates diminished the inhibitory effect of the natural preservatives on A. westerdijkiae; for P. verrucosum, their inhibitory effect increased with carbohydrates. Only the antifungal activity of trans-cinnamaldehyde did not depend on the carbohydrate content. The presence of oil had the strongest influence. At a concentration of 1% oil, the antifungal activity decreased significantly, and at 10% oil, almost no inhibition was observed. To investigate the effect of the antifungal agents on the morphology of the target molds, they were grown on malt extract agar containing carvacrol and trans-cinnamaldehyde and were examined by scanning electron microscopy. The hyphae, conidiophores, vesicles, and phialides were severely altered and deformed, and spore formation was clearly suppressed.