The global amount of soybean and wheat produced is about 350 and 750 million metric tons every year, respectively. In consequence, huge amounts of waste are produced from them. The aim of this work was to employ two wastes -soybean husk and flour mill waste- to produce high quantities of alpha-amylase enzyme. The substrate composition and the culture conditions were assayed to improve alpha-amylase production by solid-state fermentation employing the fungus Aspergillus oryzae. The maximum productivity of the enzyme was achieved using a culture substrate composed of the two wastes, at 45% soybean husk and 55% flour mill by-product, without pre-treatment, at an incubation temperature of 30 °C. The optimal incubation time (6 days), yielded a very high alpha-amylase activity (47,000 U/g dry substrate) at low-cost. The enzymatic extract obtained was characterized by LC-MS, providing a complete profile of the proteins produced during the solid-state fermentation on these two wastes. Then, the extract was purified in a single-step by size-exclusion chromatography and the recovery and the purification factor of alpha-amylase enzyme were about 83% and 6, respectively. The system was scaled up 50 times and yielded a similar enzymatic activity (45,900 U/g of dry substrate).