Glycogen serves as a primary cellular energy reserve, with its biosynthesis acting as the main strategy to cope with starvation conditions in the extracellular environment. During starvation, glycogen is either broken down in the cytosol or delivered to animal lysosomes or yeast vacuoles for degradation by macroautophagy (hereafter autophagy). However, the mechanism of glycogen autophagy remains poorly understood, particularly in the heart and skeletal muscles, which are severely affected by the lysosomal glycogen accumulation in Pompe disease. To address this knowledge gap, we developed Komagataella phaffii yeast as a simple model to study glycogen autophagy and found that it proceeds non-selectively during nitrogen starvation. In contrast, a study in Saccharomyces cerevisiae suggested that glycogen behaves as a non-preferred cargo of bulk autophagy under similar conditions. To solve this discrepancy, we utilized a new toolset of glycogen markers and clarified cargo properties of K. phaffii glycogen. Our findings revealed that both homologous and heterologous markers of glycogen are efficiently delivered to the vacuole and degraded there with a rate independent of glycogen presence. This indicates that glycogen is a neutral cargo of bulk autophagy. This work provides valuable insights into the evolutionary diversity of glycogen autophagy in yeasts, offering implications for understanding this process in muscle tissues of more complex eukaryotes. These findings may contribute to future therapeutic strategies for mitigating the pathophysiology of Pompe disease.