In this study, we reported the isolation of COOH-functionalized nanocrystal cellulose from agricultural waste, particularly dragon fruit foliage (DFF), by two methods, the citric acid/HCl acid (CA) method and the (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-mediated oxidation method. Chemical component quantification and physiochemical characterization techniques, such as FT-IR spectroscopy, XRD, TGA, XPS, and AFM, were employed to analyze DFF, bleached cellulose, and extracted CNs. We determined the contents of lignin and hemicellulose removed, while the signals for the cellulose contents remain the same for DFF-CA and DFF-TEMPO. The DLS, AFM, and SEM results indicated that the DFF-CA sample has a smaller average particle size (250 ± 50 nm) with a rod-like shape, compared to the DFF-TEMPO sample (600 ± 100 nm) with a fiber-like shape. Importantly, CNs extracted from DFF, including DFF-TEMPO, DFF-CA, and DFF-bleached, exhibited excellent properties for Cu (II) adsorption with a maximum adsorption of 227 mg·g (for DFF-CA samples), and the adsorption is almost independent of the -COOH content. Notably, we were also able to prepare Cu-containing cellulose gels showing promising antimicrobial activity. Our work opens new possibilities for the use of unexplored cellulosic byproducts in the agricultural industry as well as potential applications of Cu-containing cellulose gels as antimicrobials.