One of the biggest problems facing the use of carbon nanotubes in reinforced composites is agglomeration within the matrix phase. This phenomenon—caused by Van der Waals forces—leads to dispersion problems and weakens the properties of the composites. This research presents a multi-stage homogenization approach used to investigate the influence of the aspect ratio, volume fraction, and agglomeration of the nanofillers on the effective mechanical properties of a polymer biocomposite containing randomly dispersed carbon nanotubes and graphene nanoplatelets. The first stage consisted in evaluating the properties of the reinforced polymers by the CNT/GNP. The second step consisted in combining the reinforced polymers with different natural and synthetic unidirectionally oriented fibers. It was found that agglomeration has a huge influence on the mechanical properties of the composite. The novelty of this work consisted of the consideration of the parameters influencing the elastic properties using different micromechanics approaches and numerical techniques.