The classical production of microfibrillar cellulose involves intensive mechanical processing and discontinuous chemical treatment in solvent-based media in order to introduce additional chemical surface modification. By selecting appropriate conditions of a pulsed plasma reactor, a solvent-free and low-energy input process can be applied with introduction of microcrystalline cellulose (MCC) and maleic anhydride (MA) powders. The plasma processing results in the progressive fibrillation of the cellulose powder into its elementary microfibrillar structure and in-situ modification of the produced fibrils with more hydrophobic groups that provide good stability against re-agglomeration of the fibrils. The selection of MCC/MA ratio at above 200 % allows to separate the single cellulose microfibrils with changeable morphologies depending on the plasma treatment time. Moreover, the density of the hydrophobic surface groups can be changed through selection of different plasma duty cycle times, while the influence of plasma power and pulse frequency is inferior. The variations in treatment time can be followed along the plasma reactor, as the microfibrils gain smaller diameter and become somewhat longer with increasing plasma time. This can be related to the activation of the hierarchical cellulose structure and progressive diffusion of the MA within the cellulose microfibrils causing progressive weakening of the hydroxyl bonding. In parallel, the creation of more reactive species with time allows to create active surface sites that allow for interaction between the different fibrils into more complex morphologies. The in-situ surface modification has been demonstrated by XPS and FTIR analysis, indicating the successful esterification between the MA and hydroxyl groups at the cellulose surface. In particular, the crystallinity of the cellulose has been augmented after plasma modification. Furthermore, the AFM evaluation of the fibrils show surface structures with irregular surface roughness patterns that contribute to better interaction of the microfibrils after incorporation in an eventual polymer matrix. In conclusion, the combination of physical and chemical processing of cellulose microfibrils provide a more sustainable approach for fabrication of advanced nanotechnological materials.