This article proposes a process to prepare fully bio-based elastomer nanocomposites based on polyfarnesene and cellulose nanocrystals (CNC). To improve the compatibility of cellulose with the hydrophobic matrix of polyfarnesene, the surface of CNC was modified via plasma-induced polymerization, at different powers of the plasma generator, using a trans-beta-farnesene monomer in the plasma reactor. The characteristic features of plasma surface-modified CNC have been corroborated by spectroscopic (XPS) and microscopic (AFM) analyses. Moreover, the cellulose nanocrystals modified at 150 W have been selected to reinforce polyfarnesene-based nanocomposites, synthesized via an in-situ coordination polymerization using a neodymium-based catalytic system. The effect of the different loading content of nanocrystals on the polymerization behavior, as well as on the rheological aspects, was evaluated. The increase in the storage modulus with the incorporation of superficially modified nanocrystals was demonstrated by rheological measurements and these materials exhibited better properties than those containing pristine cellulose nanocrystals. Moreover, we elucidate that the viscoelastic moduli of the elastomer nanocomposites are aligned with power-law model systems with characteristic relaxation time scales similar to commercial nanocomposites, also implying tunable mechanical properties. In this foreground, our findings have important implications in the development of fully bio-based nanocomposites in close competition with the commercial stock, thereby producing alternatives in favor of sustainable materials.