Chitin has recently been finding novel applications in the food industry, such as antimicrobial agent in packaging, flavor enhancer, and emulsifier, and its intake as bioactive compound has show to have potential benefits in gut health, e.g., controlled lipid intake, anti inflammatory agent, and even reduced cancer risk. At the same time, deep eutectic solvents (DES) have recently gained notoriety as a green media for chitin isolation and purification, with different solvents demonstrating varying degrees of success in protein removal. Depending on the nature of its components, DES can exhibit both chao- and kosmotropic effects, with the former being leveraged to remove protein from chitin biomass. While considerable research exists on the nature and effects chao- and kosmotropic ions, little research has been done to understand the contribution of such molecules when working in tandem in DES. Herein we explore the effect seven different combinations of hydrogen bond acceptor (HBA) and donor (HBD) moieties with varying degrees of both chao- and kosmotropic properties on the separation of chitin and protein from black soldier fly (Hermetia illuciens) molt shells from their pupae stage. Samples were characterized via Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), confocal laser microscopy (CLSM), scanning electron microscopy (SEM), while protein content was determined through enzymatic hydrolysis. FTIR analysis showed that chaotropic DESs e.g., guanidine/urea and guanidine/lactic acid resulted in lower amide/hemiacetal ratios when compared to starting insect biomass, suggesting effective removal of protein fraction, while kosmotropic DESs, e.g., choline citrate/glycerol, had very little effect on this ratio. However, both groups of DES still showed a larger protein fraction than chemically treated chitin. Interestingly, protein estimation via N ₂ analysis of the protein hydrolysate, resulted in very low protein content for all DES. i.e., almost no protein was present in treated samples. This discrepancy between FTIR suggests that not all protein could be enzymatically removed. TGA analysis revealed that, for samples treated with more chaotropic solvents, this protein loss was indeed related to protein removal, as observed in the area reduction related to protein degradation. However, samples treated with kosmotropic DES presented three different degradation curves, related to chitin, protein-chitin, and protein. Confocal microscopy corroborated these results, showing protein intertwined with chitin fibers in samples treated with kosmotropic DESs. These results suggest that the kosmotropic-heavy DES led to protein-chitin reassembly or crosslinking, rather than separation, leading to underestimation of protein content from common analytical techniques.