Foxtail millet (Setaria italica L.), a millet with a smaller genome and shorter life cycle, growing in arid and semi-arid areas, is severely affected by salt stress with reduced biomass and yield. In this study, we report that salt stress poses deleterious effects on foxtail millet and in response foxtail millet shows flexibility in terms of decarboxylation under salt stress conditions. Our results indicate a significant increase in enzymatic activities as well as the expression levels of genes encoding NADP-Malic Enzyme (NADP-ME), NAD-Malic Enzyme (NAD-ME), phosphoenolpyruvate carboxykinase (PEPCK), NADP-Malate dehydrogenase (NADP-MDH), NAD-Malate dehydrogenase (NAD-MDH), Alanine aminotransferase (AlaAT) and Aspartate aminotransferase (AspAT) under salt stress. Thereby, suggesting that foxtail millet switches to mixed mode of decarboxylation mechanisms for better adaptability under salt stress. We also report that lower doses of selenium (Se) alleviated the effects of salinity. 1 µM Se supplementation enhanced the activity and gene expression of NADP-ME, NAD-ME, NADP-MDH, NAD-MDH and AlaAT. The gene expression and the activity of ATP-dependent PEPCK and AspAT were reduced by Se, making the process more energy-efficient. Hence, suggests that Se alleviated the deleterious effects of salinity by enhancing the mixed mode of decarboxylation in energy-efficient way.