The efficiency of agricultural production is key when addressing poverty and hunger in subsistence farming systems of developing countries. The transition of the subsistence systems into more productive and more sustainable land use needs to be directed by strong public interventions and investments. While policy documents for agricultural improvement often end up with a general “to do” list of recommendations, the actual effects of these technology or policy interventions are seldom evaluated for specific regions or cases. This study combines biophysical and economic research into an integrated assessment which can help to evaluate these recommendations for specific conditions. The nutrient balance model NUTMON and the Tradeoff Analysis Model are linked and subsistence farming systems in the Machakos region in Kenya are studied. The integrated modelling approach is used to evaluate a range of different policy interventions proposed in recent policy documents by the Kenyan government. This type of analysis normally requires intensive environmental and economic data collection. Therefore, new technologies for data gathering such as Digital Soil Mapping and the effect of input data resolution on model results are tested. The study clearly shows that more detailed input data are not always necessary to provide more accurate results. Policy makers can benefit from this type of methodology anticipating the possible effects of certain innovations in actual productions systems.