Graphene-based carbon sponges can be used in different applications in a large number of fields including microelectronics, energy harvesting and storage, antimicrobial activity and environmental remediation. The functionality and scope of their applications can be broadened considerably by the introduction of metallic nanoparticles into the carbon matrix during preparation or post-synthesis. Here, we report on the use of X-ray micro-computed tomography (CT) as a method of imaging graphene sponges after the uptake of metal (silver and iron) nanoparticles. The technique can be used to visualize the inner structure of the graphene sponge in 3D in a non-destructive fashion by providing information on the nanoparticles deposited on the sponge surfaces, both internal and external. Other deposited materials can be imaged in a similar manner providing they return a high enough contrast to the carbon microstructure, which is facilitated by the low atomic mass of carbon.