Soil isolate Streptomyces plicatus MK559563 succeeded in the biological conversion of agricultural wastes (rice straw RS and potato shells PS) into valuable by-products (reducing sugar and industrial enzymes) by sub merged fermentation technique (SmF). Streptomyces plicatus MK559563 xylanase and α-amylase production were statistically optimized through two designs Plackett-Burman (PB) and Central composite design (CCD). PB design showed that xylanase production by S. plicatus MK559563 was more affected by incubation time, PS weight, and (NH4)2SO4 while α-amylase production was more affected by RS weight, (NH4)2SO4, and CaCl2. CCD improved S. plicatus MK559563 xylanase and α-amylase production by 39.69 and 61.60–fold increase compared to unoptimized media. The optimized media for S. plicatus MK559563 xylanase production composed of g/L: Baker's yeast (1), (NH4)2SO4 (6.5), KCl (1), ZnSO4 (0.001) with RS (2g/flask) and PS (3.5g/flask) for 7 days of incubation. The optimized media for S. plicatus MK559563 α-amylase production composed of g/L: glucose (10), baker's yeast (5), (NH4)2SO4 (6.5), CaCl2 (6.5) with RS (3.5g/flask) and PS (1g/flask) for 6 days of incubation. Streptomyces plicatus MK559563 can be used as an intermediate step for bioconversion of agricultural wastes into biofuel.