Background/Objectives: Metal-based coordination compounds are attracting attention in medicinal inorganic chemistry because changes in the metal centre can influence their physicochemical properties and biological responses. This study aimed to evaluate two isostructural ammonium-M(II) hydrogenophosphite hydrates, (NH₄)₂[Mg(H₂O)₆]₃(HPO₃)₄ (complex 1) and (NH₄)₂[Co(H₂O)₆]₃(HPO₃)₄ (complex 2), as bioactive systems with potential anticancer and anti-inflammatory properties. Methods: The complexes were synthesized and characterized by X-ray powder diffraction (XRPD), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), density functional theory (DFT) calculations, and Hirshfeld surface analysis. Their cytotoxic activity was evaluated against B16-F10, HT29, HepG2, and HL-60 tumour cell lines. For complex 2, apoptosis, cell-cycle distribution, and mitochondrial membrane potential were analysed by flow cytometry. Nitric oxide production was measured in LPS-stimulated RAW 264.7 macrophages. Results: Complex 2 showed the highest cytotoxic activity, particularly against HL-60 leukaemia cells (IC₅₀ = 36.98 μg/mL), whereas complex 1 displayed weaker activity. Complex 2 increased apoptotic cell populations, altered cell-cycle distribution, and induced mitochondrial membrane depolarization in HL-60 cells. Both complexes reduced nitric oxide production, with complex 2 showing the strongest effect (IC₅₀ NO = 22.46 μg/mL), exceeding that of diclofenac under the experimental conditions, while complex 1 showed comparable activity to the reference drug. DFT descriptors indicated higher electronic reactivity for complex 2. Conclusions: Replacement of Mg(II) by Co(II) enhances the biological activity of this hydrogenophosphite framework. Complex 2 combines cytotoxic activity against HL-60 cells with apoptosis-associated mitochondrial dysfunction and NO-inhibitory activity in activated macrophages, supporting hydrogenophosphite-based metal complexes as bioactive coordination compounds with potential as multifunctional agents.