The role of oxygen and energy state in development and storage activity of cereal grains is an important issue, but has remained largely uninvestigated due to the lack of appropriate analytical methods. Metabolic profiling, bioluminescence-based in situ imaging of ATP, and oxygen-sensitive microsensors were combined here to investigate barley seed development. For the first time temporal and spatial maps of O2 and ATP distribution in cereal grains were determined and related to the differentiation pattern. Steep O2 gradients were demonstrated and strongly hypoxic regions were detected within the caryopsis (<0.1% of atmospheric saturation). Growing lateral and peripheral regions of endosperm remained well-supplied with O2 due to pericarp photosynthesis. ATP distribution in the developing grain was coupled to endosperm differentiation. High ATP concentrations were associated with the local onset of starch storage within endosperm, while low ATP overlapped with the hypoxic regions. Temporally, the building of steep gradients in ATP coincided with overall elevating metabolite levels, specific changes in the metabolite profiles (glycolysis and citrate cycle), and channelling of metabolic fluxes towards storage (increase of starch accumulation rate). These findings implicate an inhomogenous spatial arrangement of metabolic activity within the caryopsis. It is suggested that the local onset of starch storage is coupled with the accumulation of ATP and elevated metabolic activity. Thus, the ATP level reflects the metabolic state of storage tissue. On the basis of these findings, a hypothetical model for the regulation of starch storage in barley seeds is proposed.