Abstract: A 30% crude protein control diet was formulated for the Nile Tilapia, Oreochromis niloticus with fishmeal as the main protein source. The fishmeal content was replaced with soaked and cooked soybean at 25, 50, 75 and 90% equi-protein levels. Diets were designated as D1, D2, D3 and D4 respectively. Oreochromis niloticus fingerlings (mean weight, 10g) were randomly distributed at 20 fish per tank in duplicates. After seven days of acclimation, the fish were fed on the experimental diets for 21 days. Faecal collection was carried out using five different methods: siphoning directly from the aquaria, stripping by applying pressure on the intestinal section and collection of samples from three sections of the intestine: upper region, middle region and lower region. Acid insoluble ash was used as internal marker to assess digestibility of crude protein, lipid, ash and carbohydrate (NFE). In the siphoned, stripped and middle intestine collection methods fish fed diet 2 had the highest digestibility coefficients in crude protein, lipid, ash and NFE, while in the upper and lower intestine the control diet had the highest digestibility coefficients in crude protein, lipid and NFE. In samples collected from the lower intestine diet 4 had the least digestibility of all nutrients. While n the upper intestine fish on diet 3 had the least nutrient digestibility except in NFE. Diets 3 equally had the least digestibility in the siphoned diets except in NFE. In crude protein fish fed diet 2 had the highest digestibility of nutrients while those on diet 3 had the least. Highest numerical quantification of digestibility occured in the siphoned method while the least was in the stripped. This study shows that soybean inclusion levels and sampling methods have significant effects on the coefficients of digestibility.