A field experiment was carried out during the early cropping season of 2015 at the Teaching and Research Farm, Osun State University, Ejigbo campus, Nigeria. The study evaluated the effects of organic manures on fruit yield and antioxidant properties of green and orange morphotypes of Nigerian pumpkin. Pumpkin, locally called Elegede in the South-West Nigeria is used as an indigenous vegetable. Cattle and poultry manures were applied as treatments at the rates of 10 t ha–1 each, there was a control (plants that were treated with neither cattle nor poultry manure). The experiment was a factorial experiment, set out in a randomized complete block design with three replicates. At maturity, the fruits were harvested, yield data were taken and selected fruits across treatments were analyzed for antioxidant activities, phenol, flavonoids, anthocyanin and proanthocyanidin. Results showed that the orange morphotype out-yielded the green morphotype. Also, the yields of the plants that received cattle and poultry manures did not differ statistically. The antioxidant activities and parameters studied across the morphotypes were highest in the control and cattle manure but lowest in plants treated with poultry manure. For optimal yield and bioaccumulation of antioxidants in pumpkin fruits, cattle manure is preferred in the study area.