Accumulation of dairy waste and shortage of nutritious feed remain the major challenges in dairy cattle production. Such wastes may sustainably be biodegraded by black soldier fly larvae(BSFL) and housefly larvae(HFL) into forms which can be used as animal feed. This study was done to compare the capacity of using black soldier fly larvae(BSFL) and housefly larvae(HFL) to manage dairy wastes and use of such larvae as an alternative protein source for animal feed. Larval weight gain, prepupal yield, survival rate, biomass reduction rate, biomass reduction index, bioconversion rate, feed conversion ratio and nutritional composition of resultant BSF and HF prepupae raised on cow dung(CD) and dairy shed effluent(DSE) were determined. In order to ascertain whether the substrates had an effect on black soldier fly larvae (BSFL) and housefly larvae(HFL), analysis of variance (ANOVA) was used, and multiple mean comparisons at P≤0.05 were done using the Tukey HSD post-hoc test. Housefly larvae reared on DSE had the highest biomass reduction rate of 50.6% and biomass reduction index of 5.06, even though HFL had a shorter development time than BSFL (P≤0.05). Housefly prepupae reared on DSE had the highest crude protein content of 60.1 % of all the HF prepupae counterpart and BSF prepupae reared on DSE and CD (P≤0.05), Hence HF prepupae could be an alternative source of animal feed. Depending on the needs and purpose, utilization of fly larvae to manage dairy waste is viable and effective option.