In photosynthetic organisms, a smooth metabolic transition from dark to light conditions is essential for efficient CO2 fixation and growth. Dark-to-light transition leads to activation of the enzymes of the Calvin-Benson-Bassham (CBB) cycle and initiates CO2 fixation metabolism using energy and redox equivalents provided by the photosynthetic electron transfer reaction. While many enzymatic mechanisms of the light activation of the CBB cycle have been clarified to date, the metabolic distribution and dynamics underlying the smooth start of photosynthetic metabolism remain unclear. Here, we show rapid (on a time scale of seconds) dynamics of changes in absolute metabolite concentration and 13C tracer incorporation during photosynthetic induction (PI) in the cyanobacterium Synechocystis sp. PCC 6803. By combining these data, we were able to estimate time-resolved nonstationary dynamics of metabolic fluxes during PI. This novel metabolic analysis indicated that the initial step of PI consists of the reduction of 3-phosphoglycerate (3PG), a metabolite that accumulates in dark conditions; notably, this step occurs before subsequent generation of ribulose-1,5-bisphosphate (RuBP) and CO2 fixation by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). In vivo oxygen evolution measurement in the presence of a CBB cycle inhibitor further confirmed that the accumulated 3PG is a major initial substrate for RuBP generation and functions as a key electron sink before the initiation of CO2 fixation. Our results indicate a fundamental mechanism supporting the seamless activation of photosynthetic metabolism after dark-to-light transitions.