The low agricultural productivity of Rwanda reflects the poor soil fertility status caused by a low organic matter and high soil acidity that characterizes a large part of the country. Experimental trials have shown that a combined use of organic and inorganic fertilizers can increase crop yield. However, there are no guidelines for combined nutrients of different sources and qualities. Crop growth models can assist in the evaluation of the integration of organic and inorganic fertilizers. The Decision Support System for Agrotechnology Transfer (DSSAT) presents a collection of such crop models. The objective of this study was to determine alternative production activities through yield prediction of several crops under combined use of organic and inorganic fertilizers on Oxisols and Inceptisols in eastern Rwanda and to determine the best fertility management options. The DSSAT crop models were used to quantify the alternative production activities. The simulation of crop yield showed that predicted crop yield was distinctly higher than the actual yield for the current small-scale farming practices common in the region. The predicted yields for beans (Phaseolus vulgaris), groundnut (Arachis hypogaea), and cassava (Manihot esculenta) were approximately the same for all treatments, whereas the combined application of Tithonia diversifolia and Diammonium phosphate appeared to predict higher yields for maize (Zea mays) and sorghum (Sorghum bicolor). Yield prediction for all crops was higher on the Inceptisols than on the Oxisols because of the better chemical and physical conditions of Inceptisols. This is in line with reality.