A two-year study was undertaken in a tropical dryland agro-ecosystem to evaluate the effect of the application of soil amendments with contrasting chemical natures on crop productivity, grain yield, N-uptake and N-use efficiencies. The treatments involved the addition of equivalent amounts of N (80 kg N ha−1) through chemical fertilizer and three organic inputs at the beginning of the annual cycle: Sesbania aculeata shoots (high quality, C/N 16), wheat straw (low quality, C/N 82) and Sesbania+wheat straw (high and low quality combined, C/N 47), together with a control treatment. Test crops consisted of an annual sequence of rice and barley, sown in the rainy and winter seasons, respectively. Fertilizer and Sesbania inputs resulted in higher total net productivity (TNP) for the rice crop (47 % and 32 % increases over the control, respectively) than the combined (+28 %) and wheat straw treatments (+10 %). During the succeeding barley crop, maximum TNP was recorded in the Sesbania+wheat straw treatment (+52 %), followed by wheat straw (+43 %), fertilizer (+19 %) and Sesbania (+17 %). The TNP and grain yields of both crops added together were higher in Sesbania+wheat straw and fertilizer treatments compared to a single applications of either Sesbania or wheat straw. The Sesbania+wheat straw and fertilizer treatments resulted in more efficient utilization of N compared to the other treatments. Crop roots played a pivotal role in N-recovery from the soil and their N concentrations differed significantly (p < 0.05) due to the application of soil amendments. Across different treatments, crop root biomass was strongly correlated with crop N-uptake (r = 0.81, n = 10, p < 0.05), recovery efficiency (r = 0.81, n = 8, p < 0.05) and agronomic efficiency (r = 0.81, n = 8, p < 0.05). It is suggested that the combined application of high and low quality resources modulated N release, resulting in relatively higher productivity through the annual cropping cycle. Such combined inputs may prove useful in developing low input, environment friendly soil management practices in tropical dryland agro-ecosystems.