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A new diorganotin(IV) complex with the formula SnCl2(CH3)2L2 (C1a), L = 4‐NC5H4CONHPO(NCH3CH2C6H5)2, was synthesized and characterized using 1H NMR, 13C NMR, 31P NMR, 119Sn NMR and infrared spectroscopies. The molecular structure of C1a was determined using X‐ray crystallography, revealing that C1a contains hexa‐coordinated Sn(IV) centres with trans‐configuration of donor atoms around them. Each Sn(IV) atom is positioned in the centre of inversion of an octahedron. C1a forms one‐dimensional chains via two equal intermolecular PO…HN hydrogen bonds. These hydrogen bonds produce centrosymmetric rings as a supramolecular hydrogen‐bonded pattern. In order to compare the relative stability of C1a (with N‐ligated configuration) and its possible O‐ligated isomer, C1b, density functional theory calculations were performed, the results showing a preference of C1a over C1b from an energy point of view. Also, natural bond orbital analysis was carried out to obtain detailed information on the electronic features of the optimized structures. The theoretical results show that intermolecular hydrogen bonding in the crystal structure has a significant role in the stabilization of C1a, and Sn(IV) interacts more strongly with the Npy atom than the PO functional group. Furthermore, the free ligand and its complex were tested against three human cancer cell lines, i.e. human cervical carcinoma (HeLa), human prostate cancer (PC‐3) and human breast adenocarcinoma cancer (MCF‐7). C1a displays moderate to good cytotoxicity towards all three cancer cell lines. Moreover, antibacterial tests were carried out using the disc‐diffusion method, in which C1a shows high activity against selected Gram‐negative and Gram‐positive bacteria. Copyright © 2015 John Wiley & Sons, Ltd.