Morphological changes to the different components of lignocellulosic biomass were observed as they occurred during steam pretreatment by placing a pressure reaction cell in a neutron beam and collecting time-resolved neutron scattering data. Changes to cellulose morphology occurred mainly in the heating phase, whereas changes in lignin morphology occurred mainly in the holding and cooling phases. During the heating stage, water is irreversibly expelled from cellulose microfibrils as the elementary fibrils coalesce. During the holding phase lignin aggregates begin to appear and they increase in size most noticeably during the cooling phase. This experiment demonstrates the unique information that in situ small angle neutron scattering studies of pretreatment can provide. This approach is potentially useful in optimizing the heating, holding and cooling stages of pretreatments to allow the exact size and nature of lignin aggregates to be controlled in order to enhance enzyme accessibility to cellulose and therefore the efficiency of biomass conversion.