Flexible polyurethane foams filled with a fixed amount of carbon-based nanofillers, in particular multiwall nanotubes and graphenes, have been studied to clarify the influence of the morphology and functional groups on the physical properties of these polymeric foams. The effect of the carbon nanoparticles on the microphase separation has been analyzed by FT-IR spectroscopy revealing a decrease in the degree of phase separation of the segments. Variations of the glass transition temperature and an improved thermal stability were observed due to the presence of the nanoparticles. The EMI shielding effectiveness of flexible PU foams has also been enhanced, in particular for FGS nanocomposite foams.