Environmental concerns over petroleum-based plastics have driven interest in biodegradable, bio-based composites. Polylactic acid (PLA), derived from renewable feedstocks, is valued for its biodegradability and biocompatibility. However, PLA reinforced with synthetic or inorganic fillers often shows poor interfacial adhesion and limited functional properties. Recent advances focus on incorporating natural fillers from agricultural and industrial byproducts to improve both sustainability and performance. Natural fillers derived from polysaccharides, proteins, lignocellulosic biomass, and bioceramics offer an eco-friendly route to enhance the mechanical, thermal, and functional properties of PLA. This review presents a comprehensive classification of natural fillers based on their origin and discusses environmentally benign extraction and processing methods. The effect of interfacial adhesion and bio-based surface modifiers in improving filler dispersion and matrix compatibility is critically analyzed. The influence of natural fillers on key properties such as water absorption, moisture sensitivity, optical transparency, flame retardancy, and rheological behavior is systematically evaluated. Bio-based surface modifications using natural crosslinkers, plasticizers combined with green processing techniques such as reactive extrusion, electrospinning, and supercritical CO2 foaming, enhance filler dispersion and matrix compatibility. These strategies have led to significant improvements in mechanical strength, barrier properties, flame retardancy, and bioactivity. Consequently, PLA composites have potential applications in packaging, biomedical devices, water purification, electronics, and automotive components. This review presents an integrated, application-driven perspective, merging natural reinforcements with bio-based crosslinkers, compatibilizers, and functional additives. It explains the connections between composition, processing, and performance and highlighting current advancements in filler incorporation, surface engineering, and sustainable fabrication.