<p>Soil-borne phytopathogenic fungi pose a significant risk to many economically important crops due to their ability to survive in the soil for extended periods without a host. Thus, a novel Schiff base (HL), 3-(1H-indazol-5-ylimino)-1-phenylbut-1-en-1-ol, was synthesized by the condensation of 5-aminoindazole with benzoyl acetone. Its Co²⁺, Ni²⁺, and Cu²⁺ chelates were also synthesized. These compounds were characterized by FT-IR, ¹H-NMR, ¹³C-NMR, UV–Vis, EI–mass spectroscopy, XRD, TGA, magnetic susceptibility, elemental analysis, and molar conductance. The ligand possesses an enol form and functions as a monobasic bidentate through the deprotonated OH and C=N groups. The Co²⁺ and Ni²⁺ ions produced 1:1 (M:L) chelates, whereas Cu²⁺ ion produced a 1:2 (M:L) chelate. From the characterization results and the DFT method, it was revealed that the Co²⁺ chelate has tetrahedral geometry, while Ni²⁺ and Cu²⁺ chelates are octahedral. The antifungal activities of the ligand and the metal chelates were evaluated against some plant pathogenic fungi, namely, <i>Stromatinia cepivora</i>, <i>Botrytis allii</i>,<i> Rhizoctonia solani</i>, and <i>Sclerotinia sclerotiorum</i> in comparison with the commercial fungicide Tebuconazole. The Ni⁺² chelate emerged as the most potent agent that achieved 100% inhibition for the <i>S. cepivora</i> and <i>S. sclerotiorum.</i> It also caused significant morphological alterations in <i>S. sclerotiorum</i> as revealed by the SEM micrograph. The treated <i>S. sclerotiorum</i> hyphae displayed irregular, shriveled, and collapsed structures in contrast to the smooth and robust appearance of the control. The molecular docking study further confirmed that Ni²⁺ chelate strongly interacted with the active site of CYP51 protein compared with Co²⁺ and Cu²⁺ chelates and the fungicide Tebuconazole. The superior efficacy of Ni²⁺ chelate offers a promising alternative to traditional fungicides.</p> Graphical Abstract <p></p>