Super hydrophilic scaffolds of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) with 3 wt % of acetylated (CNC-Ac) and PEGylated (CNC-PEG) cellulose nanocrystals (CNC) were prepared. PHBV, PHBV/CNC-Ac, and PHBV/CNC-PEG scaffolds were characterized with respect to their morphology by scanning electron microscopy (SEM) and X-ray microtomography. The crystallinity was evaluated by differential scanning calorimetry (DSC) and the mechanical properties by uniaxial compression tests. The presence of residual solvent was identified by gas chromatography (GC), wettability measured by static contact angle and aqueous adsorption by gravimetry. All the scaffolds showed porous morphology, being that, for neat PHBV the morphology was more regular with oriented pores. The porosity was reduced by 26% with the introduction of CNC-Ac and CNC-PEG, and the compression modulus increased by 25% and 72% for PHBV/CNC-Ac and PHBV/CNC-PEG scaffolds, respectively, compared to neat PHBV. Even with lower porosities, PHBV/CNC-Ac and PHBV/CNC-PEG adsorbed 16% and 67% more water than PHBV scaffold, following the intraparticle diffusion model for all the samples. No residual solvents were found and the crystallinity was slightly increased upon addition of CNC-Ac and CNC-PEG. Therefore, the addition of CNC-Ac and CNC-PEG can improve both compressive modulus and water uptake, turning PHBV nanocomposite scaffolds suitable for tissue engineering applications.