Changes in cellulose microstructure have been proposed to occur throughout hydrolysis that impact enzyme access and hydrolysis rates. However, there are very few direct observations of such changes in ongoing reactions. In this study, changes in the microstructure of cellulose are measured by simultaneous confocal and atomic force microscopy and are correlated to hydrolysis extents and quantities of bound enzyme in the reaction. Minimally processed and never-dried cellulose I was hydrolyzed by a purified cellobiohydrolase, Trichoderma reesei Cel7A. Early in the reaction (similar to 30% hydrolysis), at high hydrolysis rates and high bound cellulase quantities, untwisting of cellulose microfibrils was observed. As the hydrolysis reaction neared completion (>80% hydrolysis), extensively thinned microfibrils (diameters of 3-5 nm) and channels (0.3-0.6 nm deep) along the lengths of the microfibrils were observed. The prominent microstructural changes in cellulose due to cellobiohydrolase action are discussed in the context of the overall hydrolysis reaction.