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The extraction of nanochitin from marine waste has attracted great industrial interest due to its unique properties, namely biodegradability, biocompatibility and as a functional reinforcing agent. Conventional acid hydrolysis isolation of nanochitin requires high temperatures and acid concentration, time and energy. Herein, for the first time, microwave irradiation method was used as an eco-friendly approach to isolate nanochitin from different sources. The isolation conditions were optimized through an experimental Box-Behnken design using surface response methodology. The data showed optimal conditions of 1 M HCl, 10.00 min and 124.75 W to obtain lobster nanocrystals; 1 M HCl, 14.34 min and 50.21 W to obtain shrimp nanocrystals; and 1 M HCl, 29.08 min and 54.08 W to obtain squid pen nanofibres, reducing time and HCl concentration. The obtained isolation yields where of 85.30, 79.92 and 80.59 % for lobster, shrimp and squid, respectively. The morphology of the nanochitins was dependent of the chitin origin, and the lengths of the nanochitins were of 314.74, 386.12 and > 900 nm for lobster, shrimp and squid pen, respectively. The thermal stability of the ensuing nanochitins was maintained after treatment. The results showed that nanochitin could be obtained by using an eco-friendly approach like microwave irradiation., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)