Six novel metal complexes of Co(II), Cu(II), and Zn(II) were synthesized using a microwave-assisted method. These complexes were derived from Schiff base ligands prepared through the condensation of 4-(p-fluorophenyl)-5-methyl-2-aminothiazole with 3-methoxysalicyldehyde (L1) and 2-hydroxynaphthaldehyde (L2). Characterization techniques, including UV–vis, IR, NMR, and HR-MS confirm the tridentate nature of Co(II), Zn(II), and bidentate nature of Cu(II) complexes. Elemental and thermogravimetric analysis showed 1:2 (M: L) stoichiometry in metal complexes. Meanwhile, magnetic susceptibility and powder X-ray diffraction express the geometry and crystal systems of complexes. The antimicrobial analysis of the synthesized compounds indicates Cu(II) complexes have greater potency against gram-positive bacterial and fungal strains while Zn(II) complexes show a greater zone of inhibition against gram-negative bacterial strains. Moreover, MIC values of the most potent complexes [Cu(L2)2] and [Zn(L2)2] range from 190-375 µg/mL. Furthermore, ligands and their complexes have been tested for anticancer potential against MDA-MB 231 and A549 cell lines by MTT assay. [Zn(L1)2] and [Zn(L2)2] complexes were found to have potent activity with IC50 values of 16.7 µM, 24.1 µM, and 8.7 µM, 13.4 µM respectively on MDA-MB-231 and A549 cell lines compared to other complexes and parent ligands. Molecular docking study performed using the PyRx 0.8 (with RF-Score V2 scoring function) program against EGFR (PDB: 5XGM) showed strong binding interactions which supports the experimental results.