Reduced soil fertility and damage from pests and diseases have contributed to a decline in productivity of cocoa (Theobroma cacao L.) smallholdings in Sulawesi, Indonesia over the last decade. In a trial on a marginal, acidic soil in South Sulawesi, young PBC123 cocoa trees were supplied with compost, mineral fertiliser (NPK fertiliser and urea) or dolomite, alone and in combination. After 20 months, the trees supplied with compost were taller, flowered more profusely and had a five-fold higher dry bean yield than other treatments. Treatments had no impact on incidence of cocoa pod borer, Phytophthora pod rot and vascular streak dieback. All of the trees supplied with compost survived, while the control, mineral-fertiliser- and dolomite-treated trees had a mortality rate of 22–45% and symptoms of interveinal necrosis. Leaf concentrations of N, P and K were within the normal range in all treatments. In the control and mineral fertiliser treatments, leaf concentrations of Ca (0.28–0.30%) and Mg (0.11–0.15%) were deficient, but were higher in trees supplied with compost (0.78–1.21% and 0.26–0.29%, respectively). The Mg/K ratio in soil-exchangeable cations and leaves was increased three-fold by the combined compost/dolomite treatment. Supplying mineral fertiliser alone resulted in 3.3 cmol kg−1 exchangeable Al, compared to 2.2 cmol kg−1 in control soils. Since 10 kg tree−1 year−1 compost was supplied, a rate that is not practical on most cocoa smallholder farms, further investigation of cost-effective applications of organic matter in conjunction with appropriate formulations of inorganic fertilisers is recommended.