In annual crops, the partitioning of photosynthates to support root growth, respiration and rhizodeposition should be greater during early development than in later reproductive stages due to source/ sink relationships in the plant. Therefore, seasonal fluctuations in carbon dioxide (CO 2 ) and nitrous oxide (N 2 O) production from roots and root-associated soil may be related to resource partitioning by the crop. Greenhouse studies used 13 C and 15 N stable isotopes to evaluate the carbon (C) partitioning and nitrogen (N) uptake by corn and soybean. We also measured the CO 2 and N 2 O production from planted pots as affected by crop phenology and N fertilization. Specific root-derived respiration was related to the 13 C allocated to roots and was greatest during early vegetative growth. Root-derived respiration and rhizodeposition were greater for corn than soybean. The 15 N uptake by corn increased between vegetative growth, tasseling and milk stages, but the 15 N content in soybean was not affected by phenology. A peak in N 2 O production was observed with corn at the milk stage, suggesting that the corn rhizosphere supported microbial communities that produced N 2 O. Most of the 15 N-NO 3 applied to soybean was not taken up by the plant and negative N 2 O production during vegetative growth and floral initiation stages suggests that soybean roots supported the reduction of N 2 O to dinitrogen (N 2 ). We conclude that crop phenology and soil N availability exert important controls on rhizosphere processes, leading to temporal variation in CO 2 and N 2 O production.