Cupuaçu (Theobroma grandiflorum (Willd. ex Spreng.) K. Schum.), a fruit native to the Amazon, is widely used in the food industry. However, it generates large amounts of shell and seed residues after processing, which are generally discarded inappropriately. We characterized cupuaçu residues to determine their potential as substrates for seedling production. Shells and fruit seeds were collected from a rural community in the municipality of Belterra, Brazil. The residues were weighed, dried, and crushed for chemical (macro and micronutrients, elemental analysis, and ash content) and physical (density and porosity) analyses. Different proportions of each residue (9:1, 3:1, 2:1, 1:1, and 0:1) were used, and soil alone was used as the control. The chemical analysis of the plant material showed that cupuaçu seed residues had higher concentrations of macro- and micronutrients among the analyzed elements when compared to the fruit shell residues. The macronutrient concentrations (P, K, Ca, and Mg) were, respectively, 5, 1.3, 2.3, and 5.6 times higher than those in the shell residues. Compared with the soil sample, the concentrations of the macronutrients (P, K, Ca, and Mg) in the shell residues were, respectively, 600, 162, 1283, and 12.35 times higher. Analysis of variance and comparison of treatment means were performed using Tukey’s test (p ≤ 0.05). Chemical analysis showed that cupuaçu seed and shell residues had higher concentrations of macro- and micronutrients than soil. All proportions tested with residues had lower densities and greater porosities than soil. The cupuaçu residues showed desirable chemical and physical characteristics for their use as substrate in seedling production.