A theoretical methodology and study of charge transport through GNRs, as well as in metallic and semiconducting CNTs, with randomly distributed functional groups covalently attached to the system surface is presented. By resorting to both first principles calculations, to obtain a suitable parametrization of the electronic structure, and a fully ab initio transport approach calculation to explore conduction regimes through large and disordered systems. The quantum transport modeling is based on the Green function formalism, combining an iterative scheme for the calculation of transmission coefficients with the Landauer formula for the coherent conductance. The results describe how the conductance of the hybrid systems is altered as a function of incident electron energy and molecules coverage density. Comparing two different types of functional groups, transport regimes are explored. Phenyls and hydroxyl groups induce a local orbital rehybridization of the CNTs and GNRs anchor carbon atoms from sp2-type to sp3-type yielding a localized transport regime. On the other hand, carbene groups do not disrupt the original sp2 network of armchair and small diameter zigzag CNTs which allows for good conductance preservation.