Suberin, a common biomass processing waste, is a complex biopolymer and a promising source for the biorefinery of chemicals. Six different approaches for the extraction of birch outer bark suberin fatty acids (SFAs) were explored, and their application in grafting the surface of cellulose nanocrystals (CNCs) was investigated. Successful CNC functionalization was controlled with FTIR and NMR analyses. In-depth research allowed us to evaluate the interface of the nanocellulose and polymer matrix. Three structurally distinct SFA-grafted CNCs were integrated into a vegetable oil-based acrylate resin in an ultralow concentration of 0.1 wt %. Five biobased acrylic resin formulations were prepared: without reinforcement, with CNC, and with three distinct SFA-grafted CNCs. Vat photopolymerization (VP) 3D printing was utilized for sample preparation. The effects of grafted CNC components on 3D-printed samples’ thermal stability, thermomechanical properties, and wettability were evaluated in detail. CNC functionalization enhanced the interface with the polymer matrix, yielding up to a 2-fold increase in elongation and up to a 2.5-fold increase in strength in tensile and flexural tests compared to the polymeric matrix. The CNC-SFA-modified filler demonstrated performance comparable to, or even better than, petroleum-based chemical modification routes found in the existing literature. This study highlights a promising approach for green functionalization of CNCs and verifies its use in interface enhancement using a biobased acrylate matrix.