Polyaniline (PANI) is a cheap and widely used conducting polymer due to its exceptional electrical and optoelectronic properties. However, it is insoluble in conventional organic solvents and degrades at high temperatura. To improve the performance of PANI, carbon-based nanomaterials such as graphene, graphene oxide (GO) and their derivatives can be incorporated in a PANI matrix. In this work, hexamethylene diisocyanate-modified GO has been used as reinforcement to prepare PANI/HDI-GO nanocomposites by means of in situ polymerization of aniline in the presence of HDI-GO followed by ultrasonication and solution casting. The effect of the HDI-GO functionalization degree and concentration on the final properties of the nanocomposites has been explored by scanning electron microscopy (SEM), Raman spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis (TGA), tensile tests, and four-point probe measurements. An homogenous dispersion of the HDI-GO nanosheets has been found as well as very strong PANI-HDI-GO interactions via pi-pi stacking, H-bonding, and hydrophobic and electrostatic charge-transfer complexes. A continuos improvement in thermal stability and electrical conductivity was found with increasing nanomaterial concentration, the increments being larger with increasing HDI-GO degree of functionalization. The nanocomposites showed a very good combination of rigidity, strength, ductility and toughness. The approach developed herein opens up a versatile route to prepare multifunctional graphene-based nanocomposites with conductive polymers for a broad range of applications including photovoltaic organic solar cells.