In contrast to conventional approaches, which are considered to be energy- and time-intensive, expensive, and not green, herein, we report an alternative microwave-assisted ammonium persulfate (APS) method for cellulose nanocrystals (CNCs) production, under pressurized conditions in a closed reaction system. The aim was to optimize the hydrolytic-oxidative patented procedure (US 8,900,706), replacing the conventional heating with a faster process that would allow the industrial scale production of the nanomaterial and make it more appealing to a green economy. A microwave-assisted process was performed according to different time–temperature programs, varying the ramp (from 5 to 40 min) and the hold heating time (from 60 to 90 min), at a fixed reagent concentration and weight ratio of the raw material/APS solution. Differences in composition, structure, and morphology of the nanocrystals, arising from traditional and microwave methods, were studied by several techniques (TEM, Fourier transform infrared spectroscopy (FTIR)-attenuated total reflectance (ATR), dynamic light scattering (DLS), electrophoretic light scattering (ELS), thermogravimetric analysis (TGA), X-ray diffraction (XRD)), and the extraction yields were calculated. Fine tuning the microwave treatment variables, it was possible to realize a simple, cost-effective way for faster materials’ preparation, which allowed achieving high-quality CNCs, with a defined hydrodynamic diameter (150 nm) and zeta potential (−0.040 V), comparable to those obtained using conventional heating, in only 90 min instead of 16 h.