Fique (Furcraea spp.) generates both primary fibers and industrial bagasse during fiber extraction, but the potential of these two lignocellulosic streams for nanofiber production has not been adequately compared. In this study, cellulose nanofibers from fique fibers (CNF_FF) and holocellulose nanofibers from fique bagasse (HNF_FB) were isolated by sequential alkaline treatment, controlled delignification, and mechanical fibrillation using a Super Masscolloider. The resulting nanofibers were evaluated for morphology, chemical composition, structure, thermal stability, and rheological behavior. FESEM analysis showed smaller diameters for HNF_FB (25.90–36.91 nm) than for CNF_FF (52.11–93.72 nm). These findings indicate differences in fibrillation response associated with the raw material source. Chemical analysis confirmed the high α-cellulose content of CNF_FF (86.9%), whereas HNF_FB retained hemicellulose (10.85%) and residual lignin (5.66%). FTIR-ATR and TGA showed that these non-cellulosic components, together with the anatomical heterogeneity of bagasse, influenced the structural and thermal behavior of the nanofibers. Both suspensions exhibited shear-thinning behavior, consistent with entangled nanofibrillar networks. These results demonstrate that industrial fique bagasse, generated during primary fiber extraction, is a valuable underutilized feedstock for producing holocellulose nanofibers intended for sustainable material applications.