Papaya seedlings and trees are commonly affected by damping off disease in nursery bed and root rot disease in field, respectively. The investigations were carried out at the Indian Agricultural Research Institute Regional Station, Pusa, Samastipur, Bihar (India) during the years 2014–15 and 2015–16. In the first experiment, fungicides were screened to evaluate their effectiveness for the management of damping off disease in nursery bed and in second experiment, application of macro and micronutrients and soil drenching with fungicides were evaluated for their effectiveness against root rot disease and bumpiness disorder in papaya. The seed treatment with copper oxychloride resulted in 63.65% seed germination along with 96% control of seedling damping off disease, followed by metalaxyl + mancozeb with 59.13% seed germination and 94% control of seedling damping off disease in papaya. Soil drenching with metalaxyl+mancozeb resulted in 93% control of root rot disease and 48% increase in fruit yield over control, indicating their effectiveness in root rot management in papaya. Balanced fertilization with macro and micronutrients (N: P: K: Zn: B: S @ 100: 100: 100: 10: 5: 30 g/plant) reduced the level of root rot disease and completely controlled the bumpiness disorder in papaya fruit. These approaches can be combined together in a unified way for the holistic management of seedling damping off in nursery bed, root rot disease in field and bumpiness in papaya fruits. The data generated will be important for the management of damping off, root rot and bumpiness disorder in papaya on resource poor farms of eastern Gangetic plains of India.