Understanding the behavior of microcrystalline cellulose (MCC) in developing new packaging materials is a key challenge to discriminating their impact on structure-property relationships. In this study, high concentrations of MCC fibers have been twin-screw extruded with a co-matrix of Cellulose Acetate (CA, 20 wt.%) and a ductile biopolyester (Polybutylene adipate terephthalate, PBAT). Neat PBAT (n-PBAT) and PBAT-based Hybrid specimens were produced through thermocompression. The FTIR surface chemistry showed a shift and the increase of the hydroxyl band intensity from 3412 cm−1 for Hybrid 5 to 3333 cm−1 for Hybrid 30 and MCC fibers, revealing the development of hydrogen bonds (H-bonds) and the formation of MCC agglomerates with increasing MCC content. Rheological measurements showed a one-decade jump in the complex viscosity between Hybrid 10 and Hybrid 20 composites thanks to the percolation resulting from MCC agglomerates’ formation. These agglomerates were observed in SEM micrographs, where the size of the micro-voids increased from 2 µm in Hybrid 10 to 10 µm in Hybrid 30. These microvoids increasingly jeopardized the cohesion of the hybrid systems as confirmed by uniaxial tensile testings where the hybrid strain to break reduced (by 250%) with an increasing MCC content of 30 wt.%.