The study sought to investigate the impact of a holistic high-power microwave technology during all stages of the extraction on the quality, time of extraction, and degree of deacetylation (DD) of shrimp chitosan (SC) and crab chitosan (KC). The demineralization and deproteinization stages took 7 and 8 min, at 750 and 875 W, respectively. The deacetylation process was conducted at two powers, 875 W and 1250 W, for 10, 15, and 20 min. It only took 25 min at 875 W to successfully prepare chitosan with a high DD and 30 min to reach the maximum DD. The highest DDs by the potentiometric titration method, FTIR, and 1H NMR of SC were 86.6%, 86.7%, and 83%, compared to 83.8%, 82.7%, and 80% for KC, respectively. Extracted SC had 79% solubility, 14.125 kDa, a 46.57% crystallinity index, 705.40% WBC, and 434.60% FBC, against 74.5%, 16.982 kDa, 74.14%, 689.82%, and 413.20% for KC, respectively. The study proved that 30 min of holistic high-power microwave at 875 W produced low-molecular-weight chitosan with relatively high deacetylation and low content of viscosity, crystallinity, and protein residue. The technique can provide a feasible alternative to the commercial production of low-molecular-weight chitosan in less time and energy.