Summary Glycogen is the principal carbon reserve in Synechocystis sp. PCC 6803. We reconstituted its biosynthetic pathway in vitro—GlgC (Glucose-1-phosphate adenylyltransferase), two glycogen synthase isoenzymes (GlgA1, GlgA2) and the branching enzyme GlgB—to define how supply, polymerisation and branching set flux and product structure. GlgA2 shows higher specific activity and cooperates with GlgB-generated branched primers, whereas GlgA1 has higher substrate affinity and responds more to primer concentration. Direct coupling of GlgC to GlgA establishes substrate-driven linear flux in which apparent affinity is set upstream by GlgC but the rate is limited at GlgA; increasing the GlgA : GlgC ratio relieves this bottleneck. Regulation of GlgC by 3-phosphoglycerate (activator) and inorganic phosphate (inhibitor), together with differential inhibition of GlgA, further gates flux. Product profiling links mechanism to architecture: GlgA1 produces more-branched glycogen, while GlgA2 yields longer, less-branched polymers, with GlgB biasing utilisation towards GlgA2. These findings support a two-tier control scheme—GlgC gating ADP-glucose supply and GlgA constraining utilisation—modulated by primer context and branching. The complementary behaviours of GlgA1 and GlgA2 provide capacity for rapid accumulation versus steady-state maintenance and offer dynamic metabolic levers to tune glycogen content and architecture in cyanobacteria.