The phytochemical constituents of apple waste were established as potential antifungal agents against four crops pathogens, specifically, Botrytis sp., Fusarium oxysporum, Petriella setifera, and Neosartorya fischeri. Crude, purified extracts and fractions of apple pomace were tested in vitro to evaluate their antifungal and antioxidant properties. The phytochemical constituents of the tested materials were mainly represented by phloridzin and quercetin derivatives, as well as previously undescribed in apples, monoterpene-pinnatifidanoside D. Its structure was confirmed by 1D- and 2D-nuclear magnetic resonance (NMR) spectroscopic analyses. The fraction containing quercetin pentosides possessed the highest antioxidant activity, while the strongest antifungal activity was exerted by a fraction containing phloridzin. Sugar moieties differentiated the antifungal activity of quercetin glycosides. Quercetin hexosides possessed stronger antifungal activity than quercetin pentosides.