Six new complexes of Co(II), Cu(II), and Zn(II) metal were synthesized by microwave‐assisted green method from fluorinated Schiff base ligands. The Schiff base ligands were prepared by the condensation reaction of 4‐(p‐fluorophenyl)‐5‐methyl‐2‐aminothiazole with 4‐methylsalicyldehyde (L1H) and 4‐methoxysalicyldehyde (L2H). FT‐IR, NMR, and HR‐MS spectral data confirm the tridentate nature of ligands in Co(II) and Zn(II) complexes and the bidentate nature in Cu(II) complexes. The elemental analysis and TGA study revealed 1:2 (M:L) stoichiometry in all synthesized metal complexes. Electronic absorption, magnetic susceptibility, and XRD study express the geometry and crystal systems of complexes. The antimicrobial and anticancer analysis of the synthesized ligands and their complexes were achieved. The results indicate that Co(II) and Cu(II) complexes of L2H have greater potency against Gram‐positive bacteria. In contrast, Co(II) and Cu(II) complexes of L1H exhibited greater zone of inhibition against Gram‐negative and fungal strains. Furthermore, among the synthesized ligands and their complexes, the Zn(II) complex of the L2H ligand was found to exhibit potent anticancer activity with IC50 values of 16.18 and 11.10 μM against MDA‐MB‐231 and A549 cell lines compared to other complexes and parent ligands. Molecular docking study against EGFR (PDB: 5XGM) shows strong binding interactions and good binding free energy to support the experimental results.