A new novel tetradentate ligand, [(1E,1′E)‐N,N′‐(1,2‐phenylene)bis(1‐(5‐(2‐fluorophenyl)furan‐2‐yl)methanimine) (PFPFMI), and its nano‐sized [Zn(PFPFMI)Cl2].3H2O complex were synthesized. The geometry of PFPFMI and its Zn(II) complex was described through CHN analyses, Fourier‐transform infrared spectroscopy (FTIR), UV–visible, X‐ray diffraction (XRD), thermal gravimetric analysis (TGA), and mass spectral data tests. The spectral data of the nano‐sized [Zn(PFPFMI)Cl2].3H2O complex indicates that the PFPFMI ligand functions as a tetradentate (N2O2) coordination through two azomethine nitrogen groups (N) and two furan ring oxygen (O) atoms. Density functional theory (DFT) calculations were performed using the molecular studio software to investigate the optimal geometry of PFPFMI and its [Zn(PFPFMI)Cl2].3H2O complex. The SEM, TEM, XRD, AFM, and energy dispersive X‐ray analysis (EDX) analyses of the studied complex unveil distinct and strong diffraction peaks, indicating its crystalline nature and providing evidence of its nano‐sized particle sizes. Additionally, the inhibition zone diameter was used to assess the in vitro antimicrobial action of PFPFMI and the particular complex against Gram‐positive bacteria Streptococcus pneumonia and Bacillus subtilis, Gram‐negative bacteria Pseudomonas aeruginosa, Salmonella typhi, and Escherichia coli, as well as fungi Aspergillus fumigatus, Geotricum candidum, Syncephalastrum racemosum, and Candida tropicalis. The [Zn(PFPFMI)Cl2].3H2O complex exhibits higher activity than the ligand PFPFMI. In vitro cytotoxicity of the synthesized [Zn(PFPFMI)Cl2].3H2O complex was explored using MCF7 (breast cancer), HCT116 (colon cancer), A549 (lung cancer), HePG‐2 (liver cancer), A375 (melanoma cancer), and normal lung fibroblast (WI38) cell lines. Based on IC50 and selective index (SI) values, it was shown that the complex exhibited higher potency against MCF7 cell lines. Moreover, the Zn(II) complex exhibited the ability to induce DNA damage in MCF7 cells, resulting in dose‐dependent cell apoptosis. Subsequent investigations revealed that complex 2 also induced cell cycle arrest in the G2 and S phases.