In this study, the content of chelidonine and berberine alkaloids, and sterols and phenols in the Chelidonium majus plant extract were analyzed. Subsequently, the effects of the extract on the germination and growth of Botrytis tulipae fungus on nutritive medium were compared to the effects of fluconazole. The plant extract was used at the minimum inhibitory concentration on B. tulipae developed in tulip leaves and the in vivo effects were investigated. The influence of different concentrations of C. majus extract on the physiological processes of the tulip (gas exchange parameters, photosynthetic light use efficiency, and induced chlorophyll fluorescence) were also tested to assess the applicability of the extract for the protection of ornamental plants against fungal infection. Our results demonstrated that 2% celandine extract does not significantly change the gas exchange parameters (transpiration rate, carbon dioxide uptake, and stomatal conductivity) of leaves exposed for 2 h, and does not interfere with the photochemical processes in the leaves. However, in higher concentrations, it increases the transpiration rate and net carbon dioxide influx. At concentrations of 15% and 20%, the extract lowers the potential quantum yield efficiency of photosystem II and the vitality index of the photosynthetic apparatus. Therefore we recommend the use of lower concentrations (≤6%) of celandine extract for the biological protection of tulips against gray mold.