Mitochondrial respiration and TCA cycle activity are required during salt stress in wheat to provide ATP and reductants for adaptive processes such as ion exclusion, compatible solute synthesis and ROS detoxification. However, there is a poor mechanistic understanding of how salinity affects mitochondrial metabolism, particularly respiratory substrate source. To determine the mechanism of respiratory changes under salt stress in wheat leaves, we conducted an integrated analysis of metabolite content, respiratory rate, targeted protein abundance measurements and direct enzyme activities. We showed that salt treated wheat leaves exhibit higher respiration rate and extensive metabolite changes. The activity of the TCA cycle enzymes pyruvate dehydrogenase complex and the 2-oxoglutarate dehydrogenase complex were shown to be directly salt sensitive. Multiple lines of evidence showed that the GABA shunt was activated under salt treatment. From this we can conclude that during salt exposure, key metabolic enzymes required for the cyclic operation of the TCA cycle are physiochemically inhibited by salt. This inhibition is overcome by increased GABA shunt activity, which provides an alternative carbon source for mitochondria that bypasses salt-sensitive enzymes to facilitate the increased respiration seen in wheat leaves exposed to salt.