One of the objectives of the malting industry is to reduce the energy cost during kilning without major effect on malt quality. In this study, the impact of a low hydration steeping process on lipid transfer protein (LTP1) modifications and beta-glucan breakdown was evaluated in low (LH) and high (HH) hydrated malts. LTP1 modifications analyzed by MS/MS revealed acylation, glycation, and disulfide bond breakage in both LH and HH malts. LTP1 free amine content measurement and fluorescence of Maillard protein adducts revealed no significant difference between LH and HH malts. Immunolabeling of LTP1 during malting highlighted the diffusion of the protein from the aleurone layer to the endosperm at the end of steeping in both LH and HH malts. By contrast, a significant higher amount of beta-glucans was measured in LH malts after five days of germination, whereas no significant difference between LH and HH malts was revealed through immunostaining of beta-glucans or evaluation of the endosperm integrity after seven days of germination. The possibility to reduce the effects of a low hydration steeping process on beta-glucan hydrolysis by increasing germination time was discussed.