A strategy to optimize the labeling of the reducing end of native cellulose nanocrystals (CNCs) with gold nanoparticles (AuNPs) was developed and used to investigate the arrangement of the elementary crystallites constituting these biosourced particles. First, CNCs pre-functionalized with thiosemicarbazide molecules were reacted with presynthesized AuNPs. A second method consisted in synthesizing AuNPs in situ from soluble gold derivatives in the presence of CNCs regioselectively functionalized with thiosemicarbazide molecules. Transmission electron microscopy images revealed that the direct reaction resulted in a low labeling yield and the undesired formation of AuNP aggregates. Oppositely, unprecedent high labeling yields were achieved through the in situ growth approach, with a vast majority of CNCs bearing one or several AuNPs on one end. These results evidence that cotton-derived CNCs are composed of the unidirectional assembly of chemically polar elementary crystallites, implying that the acid hydrolysis isolates fragments of microfibril bundles present in the cell walls.