The isolation of chitin utilizing ionic liquid 1-ethyl-3-methylimidazolium acetate has been determined to result in polymer contaminated with proteins. For the first time, the proteins in chitin extracted with ionic liquid have been quantified; the protein content was found to vary from 1.3 to 1.9% of the total weight. These proteins were identified and include allergenic proteins such as tropomyosin. In order to avoid 'traditional' hydroxide-based deproteinization of chitin, which could reduce the molecular weight of the final product, alternative deproteinization strategies were attempted. Testing of the previously reported deproteinization method using aqueous K3PO4 resulted in protein reduction by factors varying from 2 to 10, but resulted in significant phosphate salt contamination of the final product. Contrarily, the incorporation of GRAS (Generally Recognized as Safe) compound Polysorbate 80 into the polymer washing step provided the polymer of comparable purity with no contaminants. This study presents new options for the deproteinization of chitin that can replace traditional approaches with methods that are environmentally friendly and can produce high purity polymer.