Santolina chamaecyparissus L. (cotton-lavender; family Asteraceae), traditionally valued in medicine and cosmetics for its bioactive compounds, was evaluated for its phytochemical profile and antifungal properties against two emerging plant pathogens. Flower extracts were prepared using methanol/water (1:17 v/v) with ultrasonication and characterized through gas chromatography-mass spectrometry (GC-MS) and Fourier-transform infrared (FTIR) spectroscopy. The extract's antifungal efficacy against Neocosmospora falciformis and N. keratoplastica was assessed through both in vitro assays and in planta experiments on zucchini (cv. Diamant F1) and tomato (cv. Optima F1) using root-dipping treatments. GC-MS analysis revealed a diverse sesquiterpenoid profile, with nuciferol (17.7%), 2,1,3-benzothiadiazole (10.3%), and 8-cedren-13-ol (5.9%) as major components, alongside aromadendrane derivatives including spathulenol, viridiflorol, and ledol. The extract exhibited potent antifungal activity with minimum inhibitory concentrations (MICs) of 1500 and 1000 μg/mL against N. falciformis and N. keratoplastica, respectively. In greenhouse trials, treatment with 3000 μg/mL extract (2×MIC) effectively suppressed N. falciformis-induced wilt and root rot in both crops without phytotoxic effects. These results indicate an antimicrobial activity comparable to that of fosetyl-Al and higher than that of azoxystrobin conventional fungicides, and demonstrate the potential of S. chamaecyparissus flower extract as a sustainable, biorational alternative for managing Neocosmospora species and related pathogens in agricultural disease control.