Fruit rots caused by filamentous fungi such as Monilinia fructicola and Monilinia laxa have a strong impact on crop yield and fruit commercialization, especially as they affect a wide variety of stone fruits. The antifungal efficacy of benzylidene-cycloalkanones has been previously described in in vitro assays against M. fructicola; so, this study aims to evaluate the in vivo inhibitory potential of these hybrids on fruits that have been inoculated with M. fructicola, and use molecular docking to visualize the main interactions of these molecules in the active site of the enzyme succinate dehydrogenase (SDH). The results indicate that compound C achieves the highest inhibition of both Monilinia species (15.7–31.4 µg/mL), spore germination in vitro (<10 µg/mL), and has promising results in vivo, without causing phytotoxicity in fruits. The results from molecular docking suggest that hydroxyl groups play a crucial role in enhancing the binding of compound C to SDH and contribute to the formation of hydrogen bonds with amino acid residues on the enzyme active site.