Catalysts as the dynamo of chemical reactions along with solvents play paramount roles in organic transformations in long-lasting modes. Thus, developing effective and biobased catalysts in nontoxic solvents is highly in demand. In this report, carbon quantum dots (CQDs) functionalized with L-lysine (Lys-CQDs) were generated from entirely nature-derived materials; they were demonstrated to be a promising catalyst for C−N bond formation in choline chloride urea (ChCl/U), a natural deep eutectic solvent (NADES). Among a number of synthesized CQDs, Lys-CQD turned out to be a powerful catalyst in the model reaction with aniline to afford phenyl urea. This type of transformation is important because aniline as a nucleophile has low activity, and urea is a very weak electrophile but an abundant natural source of the carbonyl moiety at the same time. The optimized reaction was performed under a highly desirable condition without using tedious and toxic workup processes at a low temperature (37 °C for aliphatic amines and 60 °C for aniline derivatives), as well as by embracing the broad scope of products in good to high yields even with weak nucleophiles such as aniline. A proposed acid-activated mechanism was suggested for the model reaction that was further confirmed by detecting ammonia as the leaving group. To show further multifunctionality of the catalyst, a cascade catalysis approach was developed for synthesizing 2benzoxazolinone, which was furnished in a two-step transformation, starting from 2-aminophenol. Using X-ray crystallography, the structure of the final product in the cascade reaction was also determined. The catalyst was characterized using various analytical techniques including SEM, TEM, AFM, XRD, IR spectroscopy, UV−vis spectroscopy, DLS, and fluorescence spectroscopy. Measuring the acid/base sites by back titration, the catalyst was shown to be highly functionalized by the lysine functional group. The size of the catalyst was determined to be in the range of 1−8 nm, having a well-dispersed surface. In all, Lys-modified CQD, as a metal-free catalyst, was synthesized, characterized, and optimized for carbonylation, as well as a cascade reaction, under mild conditions. The whole process including catalyst synthesis and organic transformations is economically competitive and fulfills all requirements toward viability.