A novel azo dye ligand, formed by the coupling of 5‐aminosalycalic acid (mesalamine drug) with 2‐amino pyrimidine (H₂L) and its Co²⁺, Ni²⁺, and Cu²⁺ complexes, was synthesized. The structures of ligand and its complexes have been described by elemental analysis, inductively coupled plasma (ICP), thermogravimetric analysis (TGA), magnetic moment measurements, molar conductance, ultraviolet–visible (UV–Vis), X‐ray powder diffraction, infrared (IR), ¹H‐nuclear magnetic resonance (NMR), ¹³C NMR, and electron impact (EI) mass spectral studies. The obtained data detected that the H₂L ligand acts as monobasic tridentate via C=N, azo nitrogen, and deprotonated OH groups. The data supported the formation of 1:2 (M:L) for Co²⁺ complex, while Ni²⁺ and Cu²⁺ gave 1:1 (M:L) complexes mononuclear formulation. The Co²⁺ and Ni²⁺ complexes have octahedral structures, while Cu²⁺ complex has tetrahedral geometry. The ligand and its Co²⁺, Ni²⁺, and Cu²⁺ complexes were applied as an antifungal against a set of root rot‐associated soil‐born phytopathogenic fungi and compared with the effect of Hatric (recommended fungicide). Our findings revealed that the metal complexes exhibited greater antifungal activity than the parent ligand. The Cu²⁺ complex was found to be the most effective compound. The effect of Hatric and Cu²⁺ complex on structural alterations of Fusarium semitectum was studied by scanning electron microscopy (SEM).