Although the removal of lignin and hemicelluloses from cellulose pulp to produce fully bleached cellulose nanofibrils (B-CNF) is the most common practice, the presence of residual lignin and hemicelluloses in raw materials for the production of lignin containing cellulose nanofibrils (LCNFs) holds several advantages. In this work, we investigated the effect of residual lignin in Eucalyptus globulus cellulose fibers on the properties of the resulting LCNFs. The stability of the colloidal suspensions was assessed by zeta-potential values and charge density analyses. Morphology of the CNFs was studied using scanning electron microscopy and atomic force microscopy. Fibril diameter and diameter distributions for CNFs with different levels of residual lignin showed a decrease on fiber diameter as the lignin content increases. Differences in the chemical composition of the CNFs was evidenced as indicated in the Fourier-transform infrared spectroscopy spectra, particularly in fingerprint region. Thermal behavior of the CNFs was not altered by the presence of lignin, as indicated by thermogravimetric analysis. Finally, the rheological behavior of the samples was evaluated observing a gel-like behavior as well as an increase of the viscosity in LCNFs with higher lignin contents.