As primary contributors to oxygenic photosynthesis, cyanobacteria intricately regulate their metabolic pathways during the diurnal cycle to ensure survival and growth. Under dark conditions, breakdown of stored energy reserves of glycogen replenishes the intermediates, especially the downstream glycolytic metabolites necessary for photosynthetic initiation upon light irradiation. The intracellular level of the intermediates is maintained throughout the dark period. However, it remains unclear how their accumulation is maintained in the dark despite the limited availability of glycogen. Here, we showed that the metabolite accumulation stability is ensured by the low activities of phosphoenolpyruvate (PEP) converting enzymes, namely PEP carboxylase and pyruvate kinase, during the dark period. Overexpression of these enzymes significantly decreased the accumulation of glycolytic intermediates after dark incubation. The oxygen evolution ability simultaneously decreased in the overexpressing strains, indicating that the dark limitation of the PEP-consuming pathway facilitates photosynthetic initiation through the maintenance of glycolytic intermediates. This finding shed light on the importance of controlling cataplerotic flux during the dark for maintaining stable operation of the Calvin cycle.