Collagen aids in the preparation of biomaterials and its stability is a key factor for these applications. In this study, phosphonium based ionic liquids (PILs) were explored for their stability effects on collagen. The rheology of collagen and UV and fluorescence spectra slackens up with the increasing concentrations. The CD and FT-IR spectra unveil the interaction of the ions in the ionic liquid with the collagen exhibiting denaturation at higher levels. At the inter-fibrillar level, concentration dependent distortion in the banding pattern of RTT collagen fiber was observed due to the chaotropicity of ions. Molecular modeling studies also reveal the ions effect on the stability of collagen and the structural deformation at higher concentrations. Our results show that the ions play an active role on the level of interaction with protein towards the stabilization or destabilization of collagen.