Controlled cellulose fragmentation and its downsizing to micro-and nanocrystals have recently captured tremendous attention to access sustainable nanomaterials. Hitherto, few functionalized cellulose derivatives have been used as fillers, and additional knowledge is needed to establish an accurate structure−performance relationship in the realm of sustainable nanocomposites. Herein, a range of phosphorylated microcellulose (MCC) and nanosized cellulose (CNC) have been prepared and used as reinforcing fillers to build transparent and flexible cellulose-filled chitosan nanostructured films. Regardless of their functionalization, all nanocellulose fillers reach good dispersion in the matrix, while those that are microcellulose aggregate slightly inside of the films. Distinctively, improved thermal stability was seen for chitosan films reinforced with cyclotriphosphazene grafted on cellulose nanocrystals (PN-CNC), where only half weight of the bioplastic was decomposed at 700 °C. Moreover, better mechanical properties were obtained using nanocellulose instead of microcellulose as fillers, with PN-CNC-filled chitosan reaching the highest value of 1.649 MPa in tensile modulus compared to 1.195 MPa for neat chitosan films. Phosphorylated cellulose fillers (P-CNC and P-MCC) also bring interesting antibacterial and intercellular catalase activities, compared to neat chitosan and unmodified cellulose-filled chitosan. In total, this study sheds light on the pivotal role of cellulose phosphorylation in improving the thermal, mechanical, and biological properties of the next generation of rationally designed bioplastics.