Aims Conventional methodology using destructive sampling, which is laborious and has poor spatial and temporal resolution, has limited our understanding of soil-plant interactions. New non-invasive tomographic techniques have the potential to significantly improve our knowledge. In this study we demonstrated the simultaneous use of PET (positron emission tomography) and CT (X-ray computed tomography) to (a) non-destructively image a whole plant growing in sand, and (b) to link the observed morphology with recently assimilated C. The PET scanner was used to detect and visualize the location of the short-lived radioisotope 11C (with a half-life of 20.4 min) taken up by the plant through 11C-labelled CO2. This provided information on carbon translocation and the metabolism of photo-assimilates in the plant as well as root structure. The CT scanners yielded data on soil and root structure. Methods A medical PET/CT scanner was used to scan a fodder radish plant growing in a pot with test soil composed of homogenous sand. We constructed an air-plant-soil controller system (APS) to control the environmental conditions, such as CO2, temperature and light during the experiment. The plant was allowed to assimilate 11CO2 for 90 min before PET scanning was initiated. We carried out PET scanning for 60 min. Subsequently, the aerial parts of the plant was cut off and the pot was rescanned using a micro-CT scanner to obtain more detailed information on structure of the root system and the growth medium structure. Results The acquired PET and CT images gave images clearly visualizing the architecture and morphology of root and soil. Using a CT scanner, we were able to detect the main taproot located at 0 to 30 mm depth. With the PET scanner, we were able to measure a signal down to 82 mm below the surface of the sand. We found the highest concentration of 11C at the position of the main root. The PET images, at different time intervals, showed the translocation and metabolisation of photo-assimilates from top to root. Using the micro-CT scanner (voxel size of 90 μm), we were able to detect roots down to 100 mm depth. These findings correlated the PET signals measured down to 82 mm depth. Conclusions We conclude that the simultaneous use of PET and CT technologies was successfully applied for soil-plant studies. The combined PET/CT technology has potential to provide new fundamental insight into soil-plant interactions and especially into the effect of abiotic stresses in spite of the limitation due to spatial resolution.