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The objective of the present work was to investigate the influence of a pre-treatment of microbial-rich digestate (liquid mesophilic anaerobic digestate – AD-supernatant) on the morphology, crystallinity, and thermal stability of cellulose pulp fiber. The six most abundant bacteria in the AD-supernatant were determined by 16S analysis. The bacteria population was comprised mostly of Bacteroides graminisolvens (66%) and Parabacteroides chartae (28%). Enzymatic activity from the bacteria partially removed the amorphous components and increased the crystallinity and crystallite size of the cellulose substrate. The fiber pulp was incubated in AD-supernatant for 5, 10, and 20 days. The X-ray diffraction data provided evidence that the amorphous portion of the cellulose was more readily and quickly hydrolyzed than the crystalline portion. The longest incubation times (20 days) resulted in substantial deconstruction of the cellulose fiber structure and decreased the thermal degradation temperature. The anaerobic digestate is inexpensive and could be used to effectively aid in the pre-treatment of cellulose on large scale transformation processes, e.g. for making biofuels, cellulose micro/nanofiber production or engineered fiber-based materials.