• The Farm Input Subsidy Program (FISP) has been implemented since 2004, yet yields for key crops have remained low due to low crop response to inorganic fertilizers, which has limited the programʼs effect on food insecurity and poverty. • The poor response is partly attributed to poor soil health and low adoption rates of soil and water conservation practices. • Using data from a decade-long nationally representative panel, we analyze joint adoption effects of input subsidies and integrated soil fertility management (ISFM) on crop income and nutrition. • Participation in FISP is positively correlated with adoption of ISFM practices, including conservation agriculture, soil and water conservation, and organic fertilizers. • Joint use of input subsidies and ISFM practices is positively correlated with higher crop income and improved household nutrition. • Policy proposals to address low productivity and nutritional insecurity are highlighted