Cellulose nanofibrils (CNFs) are a renewable and facile to produce nanomaterial that recently gained a lot of attention in soft material research. The nanostructural properties of the fibrils largely determine their self-organizing functionalities, and the ability to tune the CNF nanostructure through control of the processing parameters is therefore crucial for developing new applications. In this study, we systematically altered the CNF production parameters (i.e., variation in cellulose source, chemical, and mechanical treatment) to observe their impact on the nanostructural properties of the resulting fibrils. Atomic force microscopy (AFM) allowed detailed topological examination of individual CNFs to elucidate fibril properties such as contour length, kink distribution and the right-handed twist periodicity of individual fibrils. Statistical analysis revealed a large dependency of the fibril properties on the industrial treatment of the cellulose source material. Our results furthermore confirm that the average charge density of the fibrils regulates both contour length and twist periodicity and, thus, has a very strong impact on the final morphology of CNFs. These results provide a route to tune the detailed nanostructure of CNFs with potential impact on the self-organization of these biological colloids and their optimal use in new nanomaterials.