Natural Fiber Welding (NFW) is a versatile biopolymer manipulation process that uses ionic liquids (ILs) to disrupt the intermolecular interactions between polymer strands. NFW enables the reconfiguration of biopolymer material structure as well as the integration of functional materials within the biopolymer matrix. This process is thought to require ILs that have both chaotropic anions and hydrogen bond donating cations, with past work focusing on ILs that have been shown to be solvents capable of the full dissolution of biopolymer materials (e.g. cotton, silk, linen, and keratin). In the present work, we looked to expand the suite of ILs that could be used for NFW by investigating the impact of IL structure and composition on the NFW process with emphasis placed on studying the impact of cation structure. Fluorescently labeled cotton yarns were exposed to selected ILs under controlled time, temperature, and atmospheric conditions. Confocal fluorescence microscopy and scanning electron microscopy were used to evaluate the level of welding in the IL-treated cotton yarns, and atomic force microscopy and tensile strength testing were used to evaluate changes in the physical properties of the welded yarns. Initial results indicate that NFW may not require the use of an IL with a hydrogen bond donating cation as long as a chaotropic anion is present.