In East Africa, soil nutrient depletion and low yields jeopardise the food security of smallholder farming families and exacerbate poverty. The main reasons for the depletion of soil nutrients are overuse due to population growth, limited land, and increasing uncertainty in agricultural production caused by climate change. This study aims to analyse and optimise nutrient flows and stocks in the homegardens of smallholder banana-coffee-based farming systems in the Kagera region in NW Tanzania. The plant nutrients nitrogen (N), phosphorus (P), and potassium (K) in plant-based biomass and organic farm waste are under investigation. We used data from a farm household survey (150 households) and from focus group discussions with 22 trainers who had been training about 750 farm households in sustainable land management (SLM) at a local farmer field school. In total, we identified six farm household types and calculated a nutrient balance (NB) for the homegardens of each household type. The NB was calculated for the following five management scenarios: S0: business as usual; S1: the use of 80% of the available human urine; S2: the incorporation of 0.5 t yr⁻¹ of the herbaceous legume species Crotalaria grahamiana into the soil; S3: the production of 5 m³ yr⁻¹ CaSa-compost (human excreta and biochar) and its application on 600 m² land; and S4: a combination of S1, S2, and S3. The results show that the NB varies considerably depending on whether farmers have implemented the SLM training, apply nutrient-preserving manure collection and storage methods, and purchase fodder (imported nutrients), or whether they do not collect manure or do not purchase fodder. Trained farm households are more likely to have a positive NB than untrained households because they have already improved the nutrient management of their farms through the successful implementation of SLM practices. Untrained households would improve the NB in their homegardens under all management scenarios. However, the NB depends on labour-intensive manure collection and compost production, labour shortages, prolonged dry seasons, and socio-economic imbalances. As long as these constraints remain, nutrient deficiencies will not be overcome with mineral fertilisers alone, because soils have to be further enriched with organic matter first. In this paper, we also emphasise the importance of the system boundary, because only a complete NB can give an estimate of actual nutrient removal and the resulting nutrient demand (including removals by fodder and trees). Further improvements in the SLM training may be achieved by (i) measuring the current nutrient status of soils, (ii) analysing the need for the coexistence of free-range livestock on the grassland and zero-grazing in trained households, and (iii) conducting an in-depth analysis of the socio-economic differences between successful and unsuccessful households. In conclusion, if smallholder farmers were to integrate further improved SLM training and optimised nutrient management (S1 to S4), we assume that the NB would turn positive. Last but not least, the SLM training by the farmer field school may serve as a best-practice example for training and policy recommendations made by government institutions.