The structure of ordered mesoporous carbons (OMC) synthesized with sucrose, furfuryl alcohol or acenaphthene using the SBA-16 mesoporous silica template with cubic Imm structure has been investigated with X-ray powder diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and N2 adsorption. This work shows that, in contrast to carbons prepared from sucrose by using SBA-15 silica as template, the impregnation of SBA-16 with sucrose failed to produce OMC with cubic Imm structure. However, when furfuryl alcohol and acenaphthene were used as carbon precursors, the cubic Imm structure was retained in the products. Thus, the latter carbon precursors were more suitable than sucrose for the formation of rigidly interconnected carbon bridges through narrow apertures of the cage-like siliceous SBA-16 mesostructure. In particular, the use of furfuryl alcohol as carbon precursor allowed us to control the degree of mesopore filling in SBA-16 and consequently, to synthesize hollow or fully filled cage-like silica–carbon mesostructures as was done in the case of channel-like SBA-15. In the case of acenaphthene only fully filled mesostructures were formed but with a much higher degree of graphitization. In the present work, we took advantage of the recent developments in the synthesis of SBA-16 with tailored diameter and entrance size of mesopores and made a step forward in the fabrication of OMC by using cage-like mesoporous silicas with narrow interconnections as templates.