In smallholder farming systems, especially in mountainous areas, households face trade-offs between meeting short-term human needs and ensuring long-term soil productivity. Improved biomass management can help break the downward spiral of overexploitation of natural resources, land degradation, and productivity decline, and support more sustainable use of marginal land. Mixed crop/livestock systems are often carefully balanced to minimize risks. Thus, when planning interventions, profound systems knowledge is crucial. However, the data required for system characterization are often scarce, and original field studies are thus necessary. The aim of this research, a case study in Tajikistan, was to improve systems understanding of the biomass cycle in crop/livestock systems in order to quantify the obstacles to the spread of sustainable land management technologies to farming households. It aimed to establish a database and methods of rapid data collection to quantify the stocks and flows of biomass, with a focus on mass balances, and to evaluate smallholders’ biomass management options and trade-offs. Data collection included household interviews, secondary literature, and reference data sets from global sources. Trade-off analysis focused on household-level self-supply of food, fodder, and fuel by farmers with different sizes of smallholdings, and their potential for on-farm recycling of organic matter. Results indicate that food self-supply by small and medium smallholders is insufficient and fodder sources are scarce. Fodder scarcity means that application of crop byproducts to soils is unlikely. Animal dung is largely used as fuel. Firewood needs exceed on-farm wood production, leading to deforestation. The approach presented facilitates an understanding of current and potential agricultural land interventions in the crop/livestock farming systems prevailing in mountainous areas.