A two-stage process consisting of a pre-acidification unit and an Upflow Anaerobic Sludge Blanket (UASB) reactor (UASBT-S) was compared with a one-stage UASB reactor (UASBO-S) to evaluate the treatment stability of starch wastewater (SW). The Two-stage process provided higher treatment stability than UASBO-S. Sludge floatation occurred in the UASBO-S when the organic loading rate (OLR) was increased to 4 g-COD/L/d, beyond which a paste-like membrane structure adhered to the granules was observed. Further analysis suggests that the substrate derived polysaccharide components embedded in the loosely-bound extracellular polymeric substances (LB-EPS), triggered significant increase in the protein/polysaccharide ratio in the tightly-bound EPS (TB-EPS), and was suggested to result in the granules floatation and disintegration. During the pre-acidification, the starch was mainly converted to acetic and propionic acids. The pre-acidification was beneficial for reducing the EPS content fluctuations in the UASBT-S, which greatly improved settling capability and strength of the granular sludge.