Within legume root nodules, rhizobia differentiate into bacteroids that oxidise host-derived dicarboxylic acids, which is assumed to occur via the TCA-cycle to generate NAD(P)H for reduction of N2. Metabolic flux analysis of laboratory grown Rhizobium leguminosarum showed that the flux from 13C-succinate was consistent with respiration of an obligate aerobe growing on a TCA-cycle intermediate as the sole carbon source. However, the instability of fragile pea bacteroids prevented their steady state labelling under N2-fixing conditons. Therefore, comparitive metabolomic profiling was used to compare free-living R. leguminosarum with pea bacteroids. While the TCA-cycle was shown to be essential for maximal rates of N2-fixation, pyruvate (5.5-fold down), acetyl-CoA (50-fold down), free coenzyme A (33-fold) and citrate (4.5-fold down) were much lower in bacteroids. Instead of completely oxidising acetyl-CoA, pea bacteroids channel it into both lipid and the lipid-like polymer poly-β-hydroxybutyrate (PHB), the latter via a type II PHB synthase that is only active in bacteroids. Lipogenesis may be a fundamental requirement of the redox poise of electron donation to N2 in all legume nodules. Direct reduction by NAD(P)H of the likely electron donors for nitrogenase, such as ferredoxin, is inconsistent with their redox potentials. Instead, bacteroids must balance the production of NAD(P)H from oxidation of acetyl-CoA in the TCA-cycle with its storage in PHB and lipids.