The decomposition of lignocellulose in nature, as well as when used as feedstock in industrial settings, takes place in a dynamic system of biotic and abiotic reactions. In the present study, the impact of abiotic reactions during the storage of pretreated lignocellulose on the efficiency of subsequent saccharification was investigated. Abiotic decarboxylation was higher in steam-pretreated wheat straw (SWS, up till 1.5% CO₂) than in dilute-acid-catalysed steam-pretreated forestry residue (SFR, up till 3.2% CO₂) which could be due to higher iron content in SFR and there was no significant CO₂ production in warm-water-washed slurries. Unwashed slurries rapidly consumed O₂ during incubation at 50 °C; the behaviour was more dependent on storage conditions in case of SWS than SFR slurries. There was a pH drop in the slurries which did not correlate with acetic acid release. Storage of SWS under aerobic conditions led to oxidation of the substrate and reduced the extent of enzymatic saccharification by Cellic® CTec3. Catalase had no effect on the fractional conversion of the aerobically stored substrate, suggesting that the lower fractional conversion was due to reduced activity of the lytic polysaccharide monooxygenase component during saccharification. The fractional conversion of SFR was low in all cases, and cellulose hydrolysis ceased before the first sampling point. This was possibly due to excessive pretreatment of the forest residues. The conditions at which pretreated lignocellulose are stored after pretreatment significantly influenced the extent and kind of abiotic reactions that take place during storage. This in turn influenced the efficiency of subsequent saccharification. Pretreated substrates for laboratory testing must, therefore, be stored in a manner that minimizes abiotic oxidation to ensure that the properties of the substrate resemble those in an industrial setting, where pretreated lignocellulose is fed almost directly into the saccharification vessel.[Figure not available: see fulltext.].