Jojoba (Simmondsia chinensis (Link) Schneider) holds high industrial value and an extended cultivation trend. Despite its increased importance, there is a lack of fundamental information about its metabolic reserves and development. Our objective was to characterise metabolite allocation and fluctuations in the carbohydrate and nutrient balance of jojoba plants, as affected by fruit load and the plant's annual cycle. Metabolite profiles were performed for each organ. Soluble carbohydrates (SC) and starch concentrations were surveyed in underground and aboveground organs of high-yield and fruit-removed plants. Simultaneously, nitrogen, potassium and phosphorus were determined in the leaves to evaluate the plant's nutritional status. We found that sucrose and pinitol were the most abundant sugars in all jojoba organs. Each sugar had a 'preferred' organ: glucose was accumulated mainly in the leaves, sucrose and pinitol in woody branches, and fructose in the trunk wood. We found that fruit load significantly influenced the carbohydrate levels in green branches, trunk wood and thin roots. The phenological stage strongly affected the SC-starch balance. Among the examined minerals, only the leaf potassium level was significantly influenced by fruit load. We conclude that jojoba's nutrient and carbohydrate balance is affected by fruit load and the phenological stage, and describe the organ-specific metabolic reserves.