The decreasing supply of fossil fuels and increasing environmental concern of food waste disposal have raised interests in food waste conversation to biofuels such as butanol. Apple pomace, a food processing waste rich in carbohydrates, is a good feedstock for butanol production. The goal of this study is to present and evaluate a process to thoroughly convert apple pomace water soluble sugars (WSS) and hydrolyzed sugars from structural carbohydrates to acetone-butanol-ethanol (ABE) by fermentation. WSS was extracted from apple pomace by hot water. The solid residue was pretreated with acid or alkali followed by enzymatic hydrolysis to obtain acid hydrolyzed sugars (ACHS) or alkali hydrolyzed sugars (ALHS). Finally, WSS, ACHS, ALHS, WSS + ACHS, and WSS + ALHS were used as substrates to produce ABE by Clostridium beijerinckii P260, respectively. Acid and alkali pretreated apple pomace showed significantly (p < 0.05) higher glucose yield after cellulase hydrolysis compared with that of unpretreated apple pomace. Addition of pectinase increased hydrolyzed glucose yield by 27.9%, 26.9%, and 33.0% for acid pretreated sample, alkali pretreated sample, and unpretreated sample, respectively. Fermentation results revealed that inhibitors generated during pretreatment could negatively affect the ABE fermentation rate and titers; however, this negative effect could be alleviated by mixing the hydrolyzed sugars with water soluble sugars. A total of 202.8, 42.1, 41.4, 260.1, and 262.2 g of ABE was produced from each kg of dry apple pomace using WSS, ACHS, ALHS, WSS + ACHS, and WSS + ALHS as the substrates, respectively, based on the mass balance.