The present study investigated the antifungal potential of hydroalcoholic extracts of propolis against the causal agent of grey mould, Botrytis cinerea, by in vitro and in vivo assays. Five different propolis from different Italian regions were subjected to hydroalcoholic extraction using different ethanol concentrations and extraction methods. The preliminary bio-assay showed significant inhibitory effects on B. cinerea mycelial growth of propolis extracts obtained using 90% ethanol and subjected to sonication. The calculation of EC50 values, based on the demonstrated efficacy of non-volatile and volatile metabolites of propolis extracts, was useful to understand the main fraction involved in the antifungal activity of the samples and to perform the in vivo assay on grape and blueberry fruits. Three of the propolis extracts showed a high amount of genistein. Conversely, the other two propolis showed a fair amount of apigenin, caffeic acid, chrysin, ferulic acid, kaempferol, luteolin, p-coumaric acid and quercetin. From the volatile analysis of propolis, the main compounds detected were α-cadinol, α-eudesmol, calamenene, cadinol, benzyl acetate, benzyl benzoate and benzyl alcohol. The results suggest that propolis extracts have potential as an effective postharvest antifungal treatment, with varying degrees of efficacy depending on the extraction method and the type of propolis metabolites.