Hop cones preparations possess a wide range of biological activities including antimicrobial properties. In this work, we evaluated the effect of various organic extracts obtained from spent hops, as well as six hops flavonoids and their twenty natural and synthetic derivatives on human and plant microbial pathogens. Methylene chloride, acetone, ethyl acetate, and methanol were used as extractants. Seven flavonoids, among them two natural (α,β-dihydroxanthohumol and 8-prenylnaringenin) showed significant activity against methicillin sensitive and resistant Staphylococcus aureus and Staphylococcus epidermidis strains with the lowest MIC80 value of 0.5 µg/mL. The crude ethyl acetate, acetone, and methanol extracts from the spent hops exhibited antifungal activity against Fusarium oxysporum, F. culmorum, and F. semitectum with the lowest MIC50 of 0.5 mg/mL, while the methylene chloride extract exerted antifungal activity against Botrytis cinerea with the MIC50 of 1 mg/mL. The preparation obtained after the removal of xanthohumol from the spent hops crude extracts retained up to 95% of activity. These findings suggest that various spent hops extracts may be effective agents for the control of plant pathogens of economic importance, like Botrytis cinerea and Fusarium oxysporum, while some compounds from spent hops or their derivatives may become useful for staphylococcal infections.