Mushroom extracts have shown potential as a source of new antimicrobial agents. This study investigates the chemical profile of an aqueous ammonia extract obtained from the carpophores ofGanoderma lucidum, which grows onQuercus ilextrees, and explores its valorization as a biorational. The major chemical constituents of the extract, identified through gas chromatography–mass spectrometry, include acetamide, oleic acid, 1,2,3,4-butanetetrol, monomethyl azelate, undecane, and palmitic acid. The anti-oomycete and antifungal activity ofG. lucidumextract was evaluated againstPhytophthora cinnamomi, the primary threat toQuercusspp. in thedehesabiome, as well as three Botryosphaeriaceae fungi. In vitro tests revealed minimum inhibitory concentration (MIC) values of 187.5 μg·mL−1againstP. cinnamomiand 187.5–1000 μg·mL−1against the fungi. Furthermore, conjugation of theG. lucidumextract with chitosan oligomers (COS) synergistically enhanced its antimicrobial activity, resulting in MIC values of 78.12 and 375–500 μg·mL−1againstP. cinnamomiand the fungi, respectively. These MIC values are among the highest reported to date for natural products against these phytopathogens. Subsequent ex situ testing of the COS-G. lucidumconjugate complex on artificially inoculatedQ. ilexexcised stems resulted in high protection againstP. cinnamomiat a dose of 782 µg·mL−1. These findings support the potential utilization of this resource from thedehesaecosystem to protect the holm oak, aligning with sustainable and circular economy approaches.