Six fungicides from various chemical groups and two natural products, i.e., Biosept Active (grapefruit extract) and Beta-Chikol (chitosan) were tested in vitro against Diaporthe eres isolated from the shoots of fruit trees. The preparations were incorporated in PDA medium to provide final fungicide concentrations of 1, 10, and 100 g cm−3. Biosept Active concentrations of 0.05%, 0.075%, and 0.1%, and Beta-Chikol concentrations of 1%, 2%, and 2.5%, respectively. The antifungal activity of the preparations was evaluated based on mycelial growth of D. eres strains after 4 and 8 days of culture and changes in the morphological structures of the fungus. The highest antifungal activity was registered for thiophanate-methyl at all tested concentrations, followed by thiram, which showed the same activity but only at 100 g cm−3. Among the preparations of natural origin, Beta-Chikol was more effective against D. eres than Biosept Active. The effects achieved by the former preparation were comparable with those achieved by some of the most effective fungicides tested against D. eres.