This work proposes a new method for obtaining poly(3-hydroxybutyrate) (PHB)/microfibrillated cellulose (MC) composites with more balanced properties intended for the substitution of petroleum-based polymers in packaging and engineering applications. To achieve this, the MC surface was adjusted by a new chemical route to enhance its compatibility with the PHB matrix: (i) creating active sites on the surface of MC with γ-methacryloxypropyltrimethoxysilane (SIMA) or vinyltriethoxysilane (SIV), followed by (ii) the graft polymerization of methacrylic acid (MA). The high efficiency of the SIMA-MA treatment and the lower efficiency in the case of SIV-MA were proven by the changes observed in the Fourier transform infrared FTIR spectra of celluloses. All modified celluloses and the PHB composites containing them showed good thermal stability close to the processing temperature of PHB. SIMA-modified celluloses acted as nucleating agents in PHB, increasing its crystallinity and favoring the formation of smaller spherulites. A uniform dispersion of SIMA-modified celluloses in PHB as a result of the good compatibility between the two phases was observed by scanning electron microscopy and many agglomerations of fibers in the composite with unmodified MC. The dual role of SIMA-MA treatment, as both compatibilizer and plasticizer, was pointed out by mechanical and rheological measurements. This new method to modify MC and obtain PHB/MC composites with more balanced stiffness–toughness properties could be a solution to the high brittleness and poor processability of PHB-based materials.