A rod-like magnetic nanocomposite was successfully synthesized in this work by loading Ag and Fe₃O₄ nanoparticles onto the surface of the hydroxyapatite/MIL-101(Fe) metal–organic framework. Various techniques were used to investigate the crystalline nature, size, morphology, and magnetic and structural properties of the HAP/MIL-101(Fe)/Ag/Fe₃O₄ nanocomposite, including X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, Raman spectroscopy, field-emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), vibrating sample magnetometry (VSM), BET surface area measurements, and zeta potential analysis. The results indicate that the nanocomposite sample is composed of Ag and Fe₃O₄ nanoparticles adhered to rod-like hydroxyapatite/MIL-101(Fe). The catalytic and antibacterial abilities of the as-prepared HAP/MIL-101(Fe)/Ag/Fe₃O₄ were studied. This nanocomposite was utilized as a heterogeneous catalyst for the catalytic reduction of toxic pollutants, including 4-nitrophenol (4-NP), 2-nitrophenol (2-NP), 2,4-dinitrophenol (2,4-NP), 4-nitroaniline (4-NA), and 2-nitroaniline (2-NA) by NaBH₄ in water and at room temperature. These compounds were converted to their amine derivatives within 8–18 min with rate constant values equal to 0.2, 0.3, 0.33, and 0.47 min⁻¹, respectively. This quaternary magnetic catalyst can be easily separated from the reaction medium using an external magnetic field and reused. The synthesized nanocomposite maintained its efficiency in reducing nitroaromatic compounds after 5 runs, showing the high stability of the catalyst. Besides, the antibacterial activity of the nanocomposite against Gram-negative and Gram-positive bacteria was evaluated using the disk diffusion method. The inhibition zone diameter of the nanocomposite against Staphylococcus aureus, Staphylococcus saprophyticus, and Escherichia coli was measured to be 17, 14, and 12 mm, respectively.