Distinct subcellular pools of glycogen particles exist within skeletal muscle fibres, distributed both within and between myofibrils and can be found in proximity to, or at a distance from mitochondria. Their precise localisation may influence their degradation rate and role in muscle function. Here, we investigated how exercise at different intensities (1- and 15-min maximal exercise) with known variations in glycogenolytic rate and relative contribution from anaerobic metabolism affects the utilisation of the distinct pools. Further, we investigated how lowered carbohydrate and energy intake affected glycogen volume densities and the storage of glycogen particles (i.e., localisation, size, and number) and their subsequent utilisation during the exercises. Using a randomized, counterbalanced, cross-over design, participants performed two maximal cycle tests of either 1 (n=10) or 15 min (n=10), conducted following consumption of two distinct diets with either high or lowered carbohydrate and energy contents. Muscle biopsies fromm. vastus lateraliswere obtained before and after the exercises. Intermyofibrillar glycogen was preferentially utilised during the 1-min exercise, whereas intramyofibrillar glycogen was preferentially utilised during the 15-min exercise. The lowered carbohydrate and energy intake decreased the particle size across all subcellular pools and reduced the numerical density in the intramyofibrillar and subsarcolemmal pools, with no effects on the glycogen utilisation during the subsequent exercise. In conclusion, the distinct subcellular glycogen pools were differentially utilised during 1-min and 15-min maximal exercise. Additionally, lowered carbohydrate and energy consumption reduces particle size and numerical density, depending on subcellular localisation.