Nanoparticles often-called proto-imogolites have been identified as an intermediate in the formation process of imogolite nanotubes as early as 1979. Their composition and structure are now well documented in the case of synthetic imogolite. One specific characteristic of proto-imogolite is that they have a curved shape with a local structure close to the one of imogolite. During a growth stage, they evolve toward nanocrystals (allophane, imogolite). Their thorough characterization has so far been difficult. Using synchrotron Small Angle X-ray Scattering coupled with Raman spectroscopy, we observe that proto-imogolites form during the initial stage of the co-precipitation of aluminum and silicon molecular precursors thanks to a reorganization process. The shape of the initial proto-imogolites, before the growth stage, depends on the synthesis conditions and controls the characteristics of the final product. We show using cryo-TEM images that, at the end of the growth stage, non-tubular nanostructures continue to coexist with nanotubes. Protocols to quantify remaining non-tubular nano-objects and purify the samples are discussed.