The main objective of this study was to determine the best soil amendment and tillage practices for sustainable millet yield and grain and stover quality. The treatments included tillage practices (immediate-, late- and no-till) and soil amendments (sheep manure plus urine, manure, millet stover (stalks, leaf blades and leaf sheaths) and millet stover ash) in factorial combinations with fertilizer nitrogen levels of 0, 15 and 30 kg ha−1 plus controls. Results showed that (i) higher yields were obtained in tilled plots than in no-till plots; (ii) tillage timing may not be a significant yield determining factor; (iii) the application of animal urine resulted in significantly higher yield and greater nitrogen, phosphorus and potassium uptake than the application either of manure alone or of millet stover. Urine application (ruminant urine contains virtually no phosphorus), which elevates soil pH especially during the first week after application, may have resulted in the dissolution of phosphorus from the aluminium–iron complexes of kaolinitic clays. This is corroborated by the significantly higher phosphorus uptake from the manure-plus-urine plots than from plots amended with either manure alone or millet stover. Long-term implications of ‘mining’ soil phosphorus with repeated applications of animal urine in these fragile ecosystems remains unclear.