The elongation of photosynthesis, or functional stay-green, represents a feasible strategy to propel metabolite flux toward cereal kernels. However, achieving the above goal remains a stunting challenge in food crops. Here, we report the cloning of wheat CO2 assimilation and kernel enhanced 2 (cake2), the mechanism underlying the photosynthesis advantages, and natural alleles amiable for breeding elite varieties. We isolated cake2 from a tetraploid wheat EMS mutant library. We detected a premature stop mutation in the A-genome copy of the ASPARTIC PROTEASE 1 (APP-A1) gene (henceforth app-A1) that co-segregates with the cake2 phenotype. A splicing mutant in the B-genome homolog (app-B1) and the double mutant (app1) enhanced photosynthesis and grain size/weight. On the contrary, overexpression of APP-A1 accelerated leaf senescence and complemented the cake2 phenotype. APP-A1 A genome is an active chloroplast protease, bound and degraded PsbO, the protective extrinsic member of photosystem II (PS II). A dysfunction mutant of PsbO (psbo-2A) partially complemented the app1 double mutant, indicating PsbO’s contribution to the enhanced function of PS II and grain development in app1. Furthermore, a natural polymorphism of the APPA1 gene in common wheat reduced APP-A1’s activity and promoted photosynthesis and grain size/weight. This work demonstrates that modification in APP1 can positively affect photosynthesis and grain size and inform future steps to understand and engineer the functional stay-green phenotype. The genetic resources could propel photosynthesis and high-yield potentials in tetraploid and hexaploid wheat elite varieties.