Cellulose nanofibrils (CNF) were isolated from agro-industrial waste (corn husks and oat hulls) and market kraft pulp fibres, and a detailed comparative study was performed. Initially, the raw materials were subjected to a conventional pulping process to remove lignin and hemicelluloses. The chemical pre-treatment was based on 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO)-mediated oxidation and the mechanical treatment was carried out with a high-pressure homogenizer. An extensive characterization of the raw material and of the nanofibrillated celluloses was performed, considering structural and chemical aspects. CNF films were produced for their characterization by optical methods, laser profilometry (LP), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Considering the same pulping and chemical pre-treatment, the analyses indicated that the oxidized corn husks fibres had higher carboxylate content and thus a larger tendency to nanofibrillate compared to the oat hulls fibres. The obtained content of carboxylic acids was directly proportional to the content of cellulose in the assessed samples, confirming the selectivity of the TEMPO-mediated oxidation. The fibrillated corn husks material had a minor fraction of residual fibres (<4%) and homogeneous nanofibril width distribution (<20 nm), which is a major achievement. The homogeneous CNF morphology was confirmed by AFM analysis. Hence, this study demonstrates that the assessed agro-industrial wastes are sustainable resources for production of CNF, which may have a wide range of value-added applications.