To produce chitosan is an interesting research. Chitosan is an important polysaccharide in terms of its various applications in industries and is produced from chitin, an abundant biopolymer in crustacean shell biomass wastes. Traditional processes for chitosan manufacture are commonly based on highly concentrated alkaline or acid solutions which are, however, severely eroding and harmful to the environment. In this study, we have described a ‘greener’ method using 1-ethyl-3-methylimidazolium acetate, [Emim][OAc] ionic liquid (IL), for decrystallization of shrimp crystalline chitin flakes followed by a microwave-mediated NaOH or tetrabutylammonium hydroxide, [TBA][OH], solution-based deacetylation for chitosan production. The decrease in crystallinity in IL pre-treated chitin was confirmed by XRD and SEM analysis which subsequently benefited chitosan production with up to 85% degree of deacetylation (%DDA) in shorter time periods (1-2 hours) and lower alkaline concentrations (20-40%). The %DDA in chitin/chitosan was estimated via FT-IR and NMR analysis. Notably, we could regenerate the ionic liquids: in case of [Emim][OAc] 97 wt.% and in case of [TBA][OH] 83 wt.% could be reused. Roles of ionic liquids in the process were discussed. Molecular dynamics (MD) simulations showed the roles of [TBA]+ cations in the molecular driving forces of [TBA][OH]-induced deacetylation mechanism. The strategy promises a sustainable and milder reaction approach to the existing highly corrosive alkaline- or acid-involved processes for chitosan production.