Effective and efficient nutrient management is central to best-practice agriculture, facilitating sustainable intensification while reducing negative externalities. The application of biochar-based fertilizers (BBF) in tropical agronomy has the potential to improve nutrient management by enhancing nutrient availability and uptake. Here, we performed pot-trials with Theobroma cacao L. seedlings planted in an Oxisol with critically low phosphorus levels. Four fertilizer levels were deployed, including BBFs using micro-dosed biochar (16 g plant−1 i.e., 0.3% soil amendment w/w) charged with mineral fertilizer. Three different fertilizer-placement levels (topsoil, root-zone hotspot and root-zone layer) were evaluated. The results from the topsoil application of mineral fertilizer (farmer practice) served as the reference data. The root-zone layer application of BBF increased the aboveground biomass, total leaf area and chlorophyll content index by 56%, 222%, and 140% respectively. Foliar phosphorus levels were also significantly elevated by 53%. The N:P ratio of the foliar tissue was improved, indicating the potential of BBF to ameliorate P limitations. Thus, low dosages of biochar, which is upgraded to BBF, can considerably improve plant nutrition. Small scale technology to produce biochar can be easily adopted and integrated in T. cacao systems. We suggest that BBF production and application within tropical, perennial systems can contribute to achieving a range of sustainable development goals (SDGs), including climate action.