In this work, the poly(methyl methacrylate) (PMMA)-Iron (Fe)-Zinc (Zn) ions incorporated hydroxyapatite nanocomposite films were developed by solvent evaporation technique and exposed to nitrogen 7+ ions implantation on different fluences viz., 1 × 1015, 5 × 1015, and 1 × 1016 ions/cm2 are denoted as PFZH115, PFZH515, and PFZH116 respectively. The N7+ ion implantation modified the surface properties but did not affect the bulk properties of the films. The ion beam implantation leads to the polymer chain scission and free radical formation due to the production of localized heating. The bombardment of the low-energy ions removed the oxygen in the composite matrix resulting in the replacement of nitrogen ions. The ion-induced surface diffusion results in the orientation of polarized dipoles and the reduction of wettability. All the samples are hemocompatible. The formation of craters is due to the continuous impingement of the ion beams that paved the way for the leaching of zinc ions from the hydroxyapatite matrix leading to the increased antimicrobial activity of the films. The surface engineering led to the proliferation of fibroblast cells by 10% which made the ion beam implantation a potential way to fabricate novel bone/dental filling materials in the biomedical field.