In the present work we report that the addition of inorganic nanoparticles to MWCNT epoxy composites leads to the formation of a hybrid structures which cause different states of dispersion for the multiphase nanocomposites containing either MWCNTs and titania or MWCNTs and silica. The microstructure is characterised by titania nanoparticles attached to the surface of MWCNTs leading to an enhanced dispersion of MWCNTs. The hydrophilic surface of fumed silica nanoparticles causes the formation of independent networks of silica and MWCNTs. Therefore, the change of the state of dispersion is less pronounced compared to the MWCNT/titania structures. Changes in the state of dispersion lead to a decrease in electrical conductivity for the MWCNT/titania systems. Conversely, an almost independent behaviour was found for the MWCNT/silica nanocomposites due to their interpenetrating networks. Besides the altered state of dispersion, the hybrid structure leads synergistic effects in terms of the glass transition of the nanocomposites. Although a decrease of the glass transition temperature (Tg) is observed for the nanocomposites containing only one kind of filler, the combination of nanoparticles can reduce the decrease of Tg.