Smallholder farmers may gain notable livelihood benefits by participating in organic value chains. However, whether there are enough resources available to maintain organic production sustainably on smallholder farms in resource-poor regions is of concern. If not balanced by sufficient inputs, continual nutrient export via commodity crops will result in nutrient mining, and livelihood improvements gained by participating in profitable value chains could be negated by soil degradation in the long term. The objectives of this study were to test an integrated approach for understanding the farm-level impacts of subsystem nutrient management actions and to identify locally viable interventions for increased nutrient supply and recycling. We employ a systems analysis methodology to address the nutrient gaps on smallholder farms in Uttarakhand, India producing organic Basmati rice for an international value chain. Farmers here rely on few livestock (three to five head of cattle ha− 1) to supply nutrient inputs and are achieving smaller than potential Basmati yields. We surveyed 42 small farms (< 3.5 ha, average annual income around $1000 year− 1) and analyzed available manure stocks for nutrient contents in order to trace the farm-level flow of manure nutrients, identify vectors of avoidable nutrient loss, and systematically identify locally relevant and feasible improvements. The interventions identified as viable were reducing nutrient losses through simple and relatively cheap manure management modifications (i.e. using straw bedding to capture livestock urine, covering farmyard manure stockpiles with plastic sheeting, enclosed biogas slurry storage, and using biogas slurry for improved compost production), in situ green manuring, and purchasing farmyard manure. Cost–benefit analyses predicted that proposed interventions could increase farmers’ net profit by up to 40% while also addressing problematic nutrient gaps. While our results pertain specifically to Uttarakhand, we found that our integrated research approach worked well to address the problem of nutrient gaps on resource-poor smallholder organic farms, and believe that the strategy could be used with equal success to address similar problems in other regions.