The selection of shade trees with appropriate spacing is important for minimising their impact on nutrient accumulation by understorey cash crops in agroforestry systems. Cocoa trees may be intercropped with overstorey legume or non-legume shade trees. A legume tree and/or a non-legume timber tree with edible kernels (Gliricidia sepium and Canarium indicum, respectively) are used as shade trees in cocoa plantations particularly in Papua New Guinea. This study explored the nutrient concentrations of cocoa beans in response to both tree-shade species and shade-tree spacing regime. The study also investigated the extent to which C. indicum tree spacing altered the nutrient concentrations of canarium kernels. G. sepium trees in the study had a final spacing of 12 m × 12 m while the spacing regimes of either 8 m × 8 m or 8 m × 16 m used for C. indicum. The calcium (Ca) concentrations of cocoa beans did not differ significantly between plants located next to G. sepium and plants located next to C. indicum. Cocoa beans next to C. indicum trees with spacing of 8 m × 16 m had higher potassium (K) concentrations than those next to G. sepium trees. However, phosphorus (P) concentrations of cocoa beans next to C. indicum trees with spacing of 8 m × 8 m or next to G. sepium trees were significantly higher than those next to C. indicum trees with spacing of 8 m × 16 m. The K concentrations in cocoa beans and soil were not correlated nor were the P concentrations in cocoa beans and soil. Correlations between nutrients in leaves and cocoa beans, or between leaves and canarium kernels, were not strong. Our results suggest that cocoa and canarium trees can be intercropped successfully, and that they do not compete for soil nutrients.