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Allometric models which are used to describe the structure of trees in agroforestry systems are usually extrapolated from models developed for trees in forest ecosystems. This makes quantitative assessment of the functions of shade trees in agroforestry systems challenging since increased availability of light and space in these systems may induce structural differences from those growing under forest conditions. We addressed this issue by providing species-specific allometric information on the structural characteristics of associated shade trees on cocoa agroforestry systems and assessed if allometries conformed to theoretical predictions. At the plot level, stand and soil characteristics affecting tree structural characteristics were assessed. The study was conducted in cocoa agroforestry systems at Suhum, Ghana. The height-diameter at breast height (H-DBH) allometry had the best fits (R2 = 53–89%), followed by the crown area (CA)-DBH allometry (R2 = 27–87%) and then the CA-H allometry (R2 = 22–73%). In general, the scaling exponents of the CA-DBH, H-CA and H-DBH allometries conformed to the metabolic scaling theory (MST). However, both the CA-DBH and H-DBH allometries diverged from the geometric similarity model. Though forest tree species had similar crown areas as fruit trees, they were slenderer than fruit trees. Tree slenderness coefficients were positively correlated with soil P, Ca, Cu and the ratios (Ca + Mg):K, (Ca + Mg):(K + Na) and Ca:Mg, but not C:N while DBH and H were correlated with soil P and C:N ratio. Our results show that critical soil nutrients and their ratios affects shade tree structural attributes (e.g. slenderness and CA), which possibly restrict variations in species-specific allometries to a narrow range on cocoa systems. Furthermore, shade tree species richness and density are better predictors of relative canopy projection area (a proxy for shade intensity) than tree species diversity. In conclusion, the results have implications for shade tree species selection, monitoring of woody biomass and maintenance of biodiversity. [ABSTRACT FROM AUTHOR]