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Physical chitosan hydrogels are potential biomaterials for several biomedical applications, such as wound healing, tissue repair, and drug delivery. Controlling the microstructural organization of chitosan gels is one of the keys for monitoring the physical, mechanical, and biological properties. As a result, the main objective of the present work was to explore the microstructural organization of chitosan hydrogels in relation with the processing conditions of gelation. For this purpose, different gelation routes were studied, that is, chitosan solution neutralization of an aqueous or hydroalcoholic solution and neutralization of an alco-gel. Overall, the resulting morphology after processing was determined by the medium viscosity during neutralization and the nature and concentration of the base. The effect of these processing parameters on the morphology was evaluated mainly through small angle light scattering (SALS) measurements including in situ measurements during chitosan neutralization. As a result, we reported different bulk microstructures consisting in 200-400 nm aggregates (primary particles) agglomerated into micrometer range clusters or arranged into more organized structures, that is, forming microchannels (4-6 μm). We thus established a qualitative and quantitative relation between supramolecular morphology and gelation conditions of chitosan hydrogels.