Ionic liquids (IL) have been shown to be effective solvents for the dissolution of a wide variety of natural polymers, and new materials can be created from these natural feedstocks by processes that involve their full dissolution and subsequent reconstitution. Yet, the dissolution and reconstitution processes eliminates the native polymer structure often resulting in materials with significantly degraded physical properties when compared to the native material. However, if only the surface layers of these natural materials are mobilized through an ionic liquid facilitated process called Natural Fiber Welding (NFW), the underlying material retains its native character and mechanical properties while still allowing for significant material modification. Furthermore, the addition of functional materials (e.g. magnetic, optical, conductive) into the IL welding solution, allows for these substances to be entrained in and on the surface of the substrate imparting unique properties to the natural materials. In this work metallic nanoparticles were synthesized in linen powders by the process of incipient wetness impregnation. The linen containing nanoparticles were added to an IL and then welded to the surface of a natural polymer substrate (e.g., cotton yarn) via NFW. The morphology of the welded materials and the distribution of nanoparticles was characterized with TEM, SEM, and fluorescent imagery. Raman and infrared spectroscopies were used to evaluate the impact of the nanomaterials on the spectroscopic properties of the biocomposites, and atomic force microscopy and tensile strength testing were used to evaluate the mechanical properties of prepared composites. Using a variety of magnetic measurement techniques, we explored how nanoparticle composition and structure relate to each systems observed magnetic properties, and how some show nanomagnetic behavior at low temperature. Overall, the prepared composites maintained many of the attractive properties of the native substrates, while still exhibiting the functional properties of the entrained materials.