Nanoparticles confined in droplets of less than a picoliter are forced to organize in submicronic dry grains throughsolvent evaporation. The evolution of structures of the grains and the constituent nanoparticles during the slow dryingprocess are investigated in situ with small-angle X-ray scattering (SAXS) for the first time. The scattering results havebeen explained on the basis of the equilibrium thermodynamics of the droplets in the drying tube. We demonstratethat this technique is really efficient in describing the internal arrangement of the nanoparticles inside the dryingdroplets. Distinction between an almost homogeneous repartition of the nanoparticles in droplets and formation ofcore shell like particles even in strongly polydispersed droplets can be made using SAXS.