Carbon-based nanomaterials possess unique structural, mechanical, and electronic properties that are exploited in numerous applications. The fate of nanomaterials in living systems and in the environment is largely unknown, though there is a reason for concern. Here it is shown how the interaction of fullerene with natural phenolic acid induces cell contraction. This phenomenon has a general applicability to carbon-based nanomaterials interacting with natural amphiphiles. Atomistic simulations reveal that the self-assembly of C70-gallic acid (GA) favors aggregation. Confocal fluorescence microscopy shows that C70-GA complexes translocate across the membranes of HT-29 cells and enter nuclear membranes. Confocal imaging further reveals the real-time uptake of C70-GA and the consequent contraction of the cell membranes. This contraction is attributed to the aggregation of nanoparticles into microsized particles promoted by cell surfaces, a new physical mechanism for deciphering nanotoxicity.