Herein, we extend a technology previously developed for internalizing SWCNTs in prokaryotes, specifically unicellular Synechocystis sp. PCC 6803, to Nostoc punctiforme, a filamentous cyanobacterial strain known to differentiate into heterocysts under nitrogen starvation. Heterocysts are specialized compartments within the filament that are capable of nitrogen fixation. These compartments possess cell walls that are distinct from vegetative cells, conferring heterocysts with relatively reduced permeability and increased resistance to mechanical and osmotic stress. Using a combination of near-infrared (NIR) fluorescence, scanning electron microscopy (SEM), and Raman spectroscopy, we investigate the effects of different cell-wall architectures and SWCNT functionalizations on internalization. We specifically examine the effects of these distinct SWCNT-cell interactions on long-term cell integrity, activity, and viability. We further show that local variations in membrane structure can dictate the extent of SWCNT association and uptake in Nostoc cells. This dependency of nanoparticle internalization on cell type can be exploited for the development of novel cell-specific staining and imaging technologies.