Multi-walled carbon nanotubes (MWCNTs) are of multidisciplinary scientific interest due to their exceptional physicochemical properties and a broad range of applications. However, they are considered potentially toxic nanoparticles when they accumulate in the environment. Given their ability to oxidize resistant polymers, mycorremediation with lignocellulolytic fungi are suggested as biological alternatives to the mineralization of MWCNTs. Hence, this study involves the ability of two fungi specie to MWCNTs biotransformation by laccase and peroxidases induction and evaluation in vivo of its toxicity using Caenorhabditis elegans worms as a model. Results showed that the fungi Penicillium chrysogenum and Pleurotus ostreatus were capable to grow on media with MWCNTs supplemented with glucose or lignin. Activities of lignin-peroxidase, manganese-peroxidase, and laccase in cultures of both fungi were induced by MWCNTs. Raman, FTIR spectroscopy, HR-TEM, and TGA analyses of the residue from the cultures of both fungi revealed structural modifications on the surface of MWCNTs and its amount diminished, correlating the MWCNTs structural modifications with the laccase-peroxidase activities in the fungal cultures. Results indicate that the degree of toxicity of MWCNTs on the C. elegans model was enhanced by the structure modification associated with the fungal ligninolytic activity. The toxic effect of MWCNTs on the in vivo model of worms reveals the increment of reactive oxygen species as a mechanism of toxicity. Findings indicate that the MWCNTs can be subject in nature to biotransformation processes such as the fungal metabolism, which contribute to modify their toxicity properties on susceptible organisms and contributing to environmental elimination.