Background and aims <p>Fusarium wilt disease caused by <i>Fusarium oxysporum</i> f. sp. <i>lycopersici</i> (FOL) poses significant threats to global tomato production, exacerbated by rising resistance to synthetic fungicides and their adverse effects on soil health. This study explores a sustainable management strategy by combining clove oil with culture filtrates (CFs) of <i>Bacillus</i> amyloliquefaciens thereby suppressing pathogen, inducing plant defense response, and yield improvement.</p> Methods <p>In vitro antifungal assays assessed the efficacy of clove oil and CFs against FOL. The bioactive profile of clove oil was characterized via gas chromatography-mass spectrometry (GC–MS). Greenhouse trials for disease severity, defense response with biochemical profile of roots and leaves were performed. Field trials over two seasons assessed treatment performance under natural FOL infection.</p> Results <p>Significant in vitro mycelial growth inhibition of FOL with 100% CFs and clove oil (250 μgml⁻¹) was recorded. GC–MS analysis of clove oil identified Eugenol (56.05%) as the prominent compound. The combined treatments reduced disease severity by 88.6%, enhanced physiological traits, and strongly upregulated various genes thereby altering enzymatic and non-enzymatic activities in leaves and roots. Treated plants exhibited enhanced defense response, while field trials revealed robust disease suppression and a threefold increase in yield compared to controls.</p> Conclusion <p>The synergistic application of clove oil and CFs offers a highly effective and sustainable alternative to conventional chemical fungicides for controlling FOL. This integrated approach significantly enhances plant disease resistance and productivity thereby promoting sustainable agricultural practices which support its potential incorporation into comprehensive and holistic disease management programs.</p> Graphical abstract <p></p>