Global food security is threatened by increasing population growth and the adverse effects of climate change. To sustain the expected global population of 9.5 billion by 2050, food production must increase by at least 60%. Exploitation of the more efficient C4 mode of photosynthesis of important food crops has been suggested as a resolution for the foreseen risk as most of the cereal crops perform C3 photosynthesis which is less efficient. Wheat (Triticum aestivum L.) is one of the most widely produced cereals globally and accounts for 21% of the world’s daily dietary protein intake. Spike photosynthesis is believed to play a vital role in grain filling in wheat, with the contribution from ear photosynthesis to the total yield being 10–44%, depending on genetic and environmental factors. That is, it seems possible that different photosynthetic traits to the main photosynthetic organs may be expressed in specific sites of the same plant, although it is less prominent. Here we refer to this phenomenon as site-specific photosynthesis. It is also hypothesized that, along with photosynthesis, other vital metabolic processes such as sucrose metabolism and nitrogen (N) assimilation vary site-specifically and may play significant roles in grain quality and quantity. The magnitude of this variation in metabolic processes varies even within the same species, indicating a significant genetic difference. In addition, the site-specific variation of metabolic processes in wheat probably depends on ontogeny, being more pronounced during grain filling. Numerous studies have been conducted to elucidate photosynthesis and other metabolic pathways in the flag leaves of wheat. However, there are few site-specific studies of plant metabolic processes, and such information is essential to improve crop yield potential. Therefore, this project aimed to dissect the site-specific, genotypic, and temporal variation of key metabolic processes associated with photosynthesis using pericarps and flag leaves of three wheat genotypes (Huandoy, ...