Edible mushrooms are seen as a way of increasing dietary diversity and achieving food security in Ethiopia. The aim of this study was to develop substrates using locally available agro-industrial by-products and animal manures to enhance the production of Shiitake (Lentinula edodes) mushrooms in Ethiopia. The hypothesis was L. edodes mushroom production on seven different substrates: 100% sugarcane bagasse (S1), 80% sugarcane bagasse, 20% cow dung (S2), horse manure (S3), chicken manure (S4), cottonseed hulls (S5), sugarcane filter cake (S6), and sugarcane trash (S7). Mushroom yield and biological efficiency were significantly affected by substrate type (p < 0.05). A significantly higher yield (434.33 g/500 g of substrate) and biological efficiency (86.83%) were obtained using substrate S4 while lower yield (120.33 g/500 g) and biological efficiency (24.33%) were obtained using substrate S7 than when using other substrates. The largest first flush of mushrooms was obtained on S4, and five flushes were produced on this substrate. S4 also had the highest biological efficiency, the highest nitrogen content, and the lowest C:N. Chicken manure is rich in nitrogen, magnesium, calcium, and potassium, which are crucial for Shiitake mushroom growth. Thus, substrate S4 would be a viable option for cultivating Shiitake mushrooms, particularly in regions where chicken manure is readily available. Substrate S2 also provided high yields and rapid fructification and would be a suitable alternative for Shiitake mushroom cultivation.