Declining land productivity is a major problem facing smallholder farmers today in Sub-Saharan Africa, and as a result increase in maize grain yield has historically staggered behind yield gains that have been achieved elsewhere in the world. This decline primarily results from reduction in soil fertility caused by continuous cultivation without adequate addition of external nutrient inputs. Improved soil fertility management practices, which combine organic and mineral fertilizer inputs, can enable efficient use of inputs applied, and can increase overall system's productivity. The trials were established at two sites with different soil fertility status to determine the effects of various organic sources (Tithonia diversifolia, Mucuna pruriens, Calliandra calothyrsus and cattle manure) and their combinations with mineral fertilizer on maize grain yield, economic return and soil chemical properties. Drought spells were common during the peak water requirement periods, and during all the seasons most (90%) of the rainfall was received before 50% flowering. In good and poor sites, there was a significant (p < 0.001) effect of season on maize grain yield. Tithonia diversifolia recorded the highest (4.2 t ha−1) average maize grain yield in the poor site, while Calliandra calothyrsus gave the highest (4.8 t ha−1) average maize grain yield in the good site. Maize grain yields were lower in treatments with sole fertilizer compared with treatments that included organic fertilizers. The maize grain yields were higher with sole organics compared with treatments integrating organic and inorganic fertilizers. Soil pH increment was statistically significant in the sole manure treatment in good and poor sites (t-test, p = 0.036 and 0.013), respectively. In the poor site, magnesium increased significantly in the sole manure and manure + 30 kg N ha−1 treatments with t-test p = 0.006 and 0.027, respectively. Soil potassium was significant in the sole manure treatment (t-test, p = 0.03). Generally the economic returns were low, with negative net benefits and benefit cost ratio of less than 1. Inorganic fertilizer recorded the highest net benefit and return to labour (p < 0.001 and <0.01, respectively) in the good site. The treatments that had very high maize grain yields did not lead to improved soil fertility, thus there is need for tradeoffs between yield gains and soil fertility management when selecting agricultural production technologies.