Dihydrolipoamide dehydrogenase (LADH) is a flavo-enzyme that serves as a subunit of alpha-ketoglutarate dehydrogenase complex (alpha-KGDHC). Reactive oxygen species (ROS) generation by alpha-KGDHC has been assigned to LADH (E3 subunit) and explained by the diaphorase activity of E3. Dysfunctions of alpha-KGDHC and concurrent ROS production have been implicated in neurodegeneration, ischemia-reperfusion, and other pathological conditions. In this work we investigated the in-depth details of ROS generation by isolated LADH and alpha-KGDHC. We found a parallel generation of superoxide and hydrogen peroxide by the E3 subunit of alpha-KGDHC which could be blocked by lipoic acid (LA) acting on a site upstream of the E3 subunit. The pathologically relevant ROS generation (at high NADH/NAD+ ratio and low pH) in the reverse mode of alpha-KGDHC could also be inhibited by LA. Our results contradict the previously proposed mechanism for pH-dependent ROS generation by LADH, showing no disassembling of the E3 functional homodimer at acidic pH using a physiologically relevant method for the examination. It is also suggested that LA could be beneficial in reducing the cell damage related to excessive ROS generation under pathological conditions.