This study explores zinc-functionalized chitosan (CS) for engineering bio-multifunctional interfaces via three atomic-scale techniques: vapor phase metalation (VPM), multiple pulsed vapor phase infiltration (MPI), and O2 plasma-enhanced atomic layer deposition (PEALD). X-ray photoelectron spectroscopy (XPS) analysis and scanning electron microscopy (SEM) with integrated energy-dispersive X-ray (EDX) elemental mapping confirmed homogeneous Zn distribution in all regimes, while AFM revealed a topographical transition from planarization in VPM (Rq = 5.6 nm) to high-surface-area nucleation in MPI (Rq = 123.9 nm). X-ray diffraction (XRD) analysis demonstrated structural reconfiguration, with VPM reducing the hydrated phase crystallite size (7.4 to 4.6 nm) and MPI achieving the finest nanocrystallinity (1.83 nm). Notably, PEALD-modified interfaces exhibited the highest interfacial energy (0.102 J/m²) and enhanced swelling. Physicochemical characterization showed the functionalization method dictates semiconductor properties, while biological assays revealed C2C12 cell proliferation comparable to the control, along with tailored antiseptic activity against E. coli and H. pylori. Significantly, in vivo subcutaneous implantation revealed that CS-ZnO PEALD scaffolds act as immunomodulatory interfaces, promoting active angiogenesis and a balanced immune response with stable anti-inflammatory IL-10 levels and near-basal pro-inflammatory expression (IL-6 = 0.5 pg/mL). These findings highlight the versatility of ALD-based processes for next-generation intelligent medical implants and bio-integrated electronics.