In this work, carbon fiber composites with epoxy matrices modified with different carbon nanotubes (CNTs) contents (0.1, 0.2 and 0.3wt.%) and with different surface conditions (non-functionalized and amino-functionalized ones) have been manufactured by vacuum assisted resin infusion molding. The dispersion of the CNTs in the epoxy resin has been made using a calendering method. Multiscale composites showed an improved mechanical behavior and this effect was more evident in the case of composites filled with functionalized CNTs, mainly in the case of the mechanical properties dominated by the matrix, such as flexural strength and interlaminar shear strength (ILSS). The formation of a stronger interface between the amino-functionalized CNT and the epoxy matrix favors the stress transfer and the participation of more effective strengthening mechanisms. However, the dispersion of amino-CNTs was less effective and the presence of micro-agglomerates reduced their potential strengthening effect.