Sustainable polymer composites are progressively under development in a technological paradigm shift from "just use more and more" to "convert into value-added products". The bio-based blends based on Mater-Bi bio-plastic (A) and poly(ε-caprolactone) (B), at a weight ratio of 70:30 (A:B) were developed, followed by the addition of UFC100 cellulose (C) filler to yield 70/30 (w/w) (A:B)/C sustainable biocomposites. The effects of chemical modification of C with three diisocyanates, i.e., hexamethylene diisocyanate (HDI), methylene bisphenyl isocyanate (MDI), or toluene diisocyanate (TDI) on the surface properties of biocomposites was evaluated by water contact angle and surface roughness detected by atomic force microscopy (AFM). Biocomposites containing C modified with HDI, MDI, or TDI revealed contact angle values of 93.5°, 97.7°, and 92.4°, respectively, compared to 88.5° for reference blend, indicating enlarged hydrophobicity window. This action was further approved by increased fracture surface roughness and miscibility detected by microscopic observation (scanning electron microscopy (SEM) and AFM) and in-depth oscillatory rheological evaluation. Correspondingly, thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) analyses showed more residue and higher melting temperatures for biocomposites, more promisingly with MDI and TDI modifiers. In conclusion, either incorporation or diisocyanate modification of C affects both surface and bulk properties.