The full exploitation of the outstanding mechanical properties of cellulose nanofibrils (CNFs) as potential reinforcements in nanocomposite materials is limited by the poor interactions at the CNF-polymer matrix interface. Within this work, tailor-made copolymers were designed to mediate the interface between CNFs and biodegradable poly(butylene adipate-co-terephthalate) (PBAT), and their effect on extruded nanocomposite performance was tested. For this purpose, two well-defined amphiphilic anchor-tail diblock copolymer structures were compared, with a fixed anchor block length and a large difference in the hydrophobic tail block length. The aim was to evaluate the impact of the copolymers’ chain length on the nanocomposite interface. The presence of amphiphilic diblock copolymers significantly improved the mechanical properties compared to those of PBAT nanocomposites containing unmodified CNFs. In particular, the copolymer with a longer tail was more effective for CNF-PBAT dispersion interactions, leading to a 65% increase of Young’s modulus of neat PBAT, while retaining high deformability (670%). The results provide insights into the effectiveness of a waterborne third component at the CNF-matrix interface and its structure-property relationship.