This study addresses the growing need for sustainable and effective antibacterial agents amid rising antibiotic resistance. We developed eco-friendly silver-natural diatomite nanocomposites (Ag-NDs) from agro-industrial waste using pineapple leaf (PL) extract. The methods employed included a green one-pot synthesis using pineapple leaf extract, which resulted in AgNP-NDs-PL; a conventional calcination method, which produced AgNP-NDs-Calc; and molecular simulation to support the experimental findings. The resulting nanocomposites materials were characterized by Fourier Transform Infrared Spectroscopy (FTIR), Particle Size Analysis (PSA), X-ray Diffraction (XRD), Scanning Electron Microscopy–Energy Dispersive X-ray Spectroscopy (SEM-EDX), Thermogravimetric Analysis (TGA), and Transmission Electron Microscopy (TEM) analyses, followed by antibacterial assays and molecular simulation. The molecular simulations were performed using the Material Studio 7.0 with the calculation of adsorption energies between five major phytochemical constituents in pineapple leaf extract on (Ag(100)) surface. The AgNp-NDs-PL nanocomposites synthesized by green synthesis showed superior antibacterial activity at lower silver concentrations against Pseudomonas aeruginosa and Staphylococcus aureus at lower concentrations due to smaller nanoparticle size and phytochemical synergy. Complementary molecular simulations revealed that strong interactions between Ag(100) and 1,3-O-dicaffeoylglycerol from pineapple leaf extract. This integrated experimental-computational approach offers a novel, sustainable strategy for fabricating potent antibacterial agents aligned with circular economy principles.