DSC, attenuated total reflexion infrared (ATR-FTIR), and Raman microspectroscopy were used for the first time in a close to in vivo environment to study ready-to-spin Bombyx mori silkworms. The aim was to understand the change of the fibroin backbone organisation from the gland to the fibre. Raman shifts of the Amide I components reveal a strong change of organisation in the middle part of the hydrated gland, as anticipated previously measured modifications of salts concentrations and pH. Series of bands characteristics of the fully hydrated silk disappear, as observed for spider silk, despite the different aminoacid sequence. Confirmation is obtained from IR spectra taking into account the superimposed water component. The change of the silk water interaction in the central part of the gland, from a hydrophobic to hydrophilic behaviour, is related to the water content decrease along the gland. pH sensitive carboxylate side chains markers confirm the modification. Fibroin organisation was also studied in the dried gland and in the spun fibre. The fibre extrusion by orients the fibroin chains along the fibre axis, with intercalated water molecules, leading to a material with specific mechanical properties, compared to the amorphous dried gland.