Recent studies are increasingly focusing on quinoa (Chenopodium quinoa) as a high-quality protein-rich food source and, in general, on seed quality. This latter is a complex trait difficult to characterize with standard measurements or analyses. X-ray micro-CT allows to visualise the internal structure of small objects and has been already used in seed research, mostly for maize kernel characterization. To date this technique has not yet been applied to study quinoa seeds, despite the increasing interest for their nutritional properties. The aim of this work was to explore the use of X-ray microtomography to provide new traits improving the seed phenotyping of quinoa. Two different scanning approaches have been compared: one based on the simultaneous scanning of multiple seeds (30) at lower resolution (20 μm voxel size) and one based on the scanning of a single seed at higher resolution (2 μm voxel size). Such approaches were tested on a study case consisting of four different quinoa genotypes. Among the measured morpho-densitometric parameters, the embryo volume and weight ratios (derived from bulk and single seed scanning, respectively) showed high positive correlation with the total protein content, while the thickest fraction of the pericarp was the best correlated with the presence of saponins.