Dilute acid hydrolysis of lignocellulose often requires a neutralisation step to utilise the hydrolysate's sugars. In this context, very little is known regarding the impact of low levels of acids or their corresponding salts produced by neutralisation on the catalyst performance in the hydrogenation of sugars. In this work, the influence of a series of ammonium and alkali metal salts (that is, NH4NO3, NaNO3, (NH4)2SO4, Na2SO4 and K2SO4) on the hydrogenation of glucose and xylose is addressed. This study also encompasses “real‐world” hydrolysates obtained by the mechanocatalytic depolymerisation of α‐cellulose and beechwood. The impact of low levels of acids and their salts upon the hydrogenation of sugars to sugar alcohols (alditols) was examined, in the presence of a commercial Ru/C catalyst (Ru/C, 0.7 wt % Ru) at 110 °C using batch and trickle‐bed reactors. The results show that the presence of salts leads to a considerable decrease in the alditols yields. Notably, salt anions exert an effect stronger than that of cations in the catalyst deactivation. Surprisingly, nitrates had a more significant effect on the decrease in the alditols yield than sulfates, and chlorides had the lowest impact. In this study, we also present the effect of sugars’ degradation products (e.g. 5‐(hydroxymethyl)furfural and furfural) upon hydrogenation of lignocellulose hydrolysates. The activated carbon pre‐treatments of the hydrolysates showed a positive effect on the catalyst activity, adsorbing hydrolysis by‐products. Overall, this study has significant implications for the practical aspects of hydrogenation of lignocellulose hydrolysates, which are often neglected in the current literature.