The efficient bioconversion of the lignocellulosic agro-waste has immense importance in biorefinery processing in extracting the cellulose and saccharide fractions. To achieve this, a series of chemical pretreatments is employed, thus concerning environmental threats limit its use. Therefore, an ionic liquid is employed for pretreatment before sustainable extractions owing to its safe manipulation, recycling, and reusability. Specifically, microwave-assisted ionic liquid (MWAIL) pretreatment has significant importance in extracting high cellulose yield at less thermal power consumption. In this study, the leftover stalks of Hamelia patens were subjected to MWAIL pretreatment at 60, 70, 80, and 90 °C to extract microcrystalline cellulose (MCC). Subsequently, the MCC was fabricated into cellulose nanocrystals (CNC) through hydrolytic treatment using acidic and ionic liquids and denoted as CNC-AH and CNC-ILH. Thus obtained CNC was characterized by FTIR, FESEM, XRD, and TGA to investigate the influence of solvent on its morphology, crystallinity, and thermal stability of CNC. The results support that the CNC-ILH has comparatively more thermal and dispersal stability with a reduced crystallinity index than CNC-AH. The surprising results of CNC-ILH signify its utilization in diverse applications in the food and industrial sectors.