Since their discovery, carbon nanotubes (CNTs) have been eminent members of the nanomaterial family. Because of their unique physical, chemical and mechanical properties, they are regarded as new potential materials to bring enormous benefits in cell biology studies. Undoubtedly, the first step to prove the advantages of CNTs is to understand the basic behavior of CNTs inside the cells. In a number of studies, CNTs have been demonstrated as new carrier systems for the delivery of DNA, proteins and therapeutic molecules into living cells. However, post-uptake behavior of CNTs inside the cells has not received much consideration. Utilizing the plant cell model, we have shown in this study that the plant cells, differentiating into tracheary elements, incorporate cup-stacked carbon nanotubes (CSCNTs) into cell structure via oxidative cross-linking of monolignols to the nanotubes surface during lignin biosynthesis. This finding highlights the fate of CNTs inside plant cells and provides an example on how the plant cell can handle internalized carbon nanomaterials.