How metabolism is rewired during embryonic development of the nervous system is still largely unknown because tracing metabolic activities with spatiotemporal resolution during neurogenesis remains a major technical challenge. Here, we investigated changes in the number of active mitochondria in the developing avian retinas, focusing on the conversion of progenitors into retinal ganglion cells (RGCs). Our study uncovers how ATOH7 and HES5.3 influence the dynamic changes in the number of active mitochondria as cells transit from uncommitted to pre-committed progenitors and then to newborn RGCs. There is a transient decrease of mitochondrial activity few hours before cells become committed to the RGC fate. While there is a general trend toward fewer mitochondria when retinogenesis begins, cells that enter the RGC lineage, as well as newborn RGCs, recover the high number of active mitochondria that characterizes uncommitted retinal progenitors. We assessed metabolic dynamics at the onset of cell differentiation by monitoring changes in metabolite concentration in vivo. Combined, our approaches identify changes in metabolic activities which are intrinsically linked to cell fate determination.