Pyruvate dehydrogenase (PDH) is the first enzyme (E1) of the PDH complex (PDC). This multienzyme complex contains E1, E2 and E3 components and controls the entry of carbon into the mitochondrial tricarboxylic acid (TCA) cycle to enable cellular energy production. The E1 component of PDC is composed of an E1α catalytic subunit and an E1β regulatory subunit. In Arabidopsis thaliana, there are two mitochondrial E1α homologs encoded by IAA-Alanine Resistant 4 (IAR4) and IAR4-LIKE (IAR4L), and one mitochondrial E1β homolog. Although IAR4 was reported to be involved in auxin conjugate sensitivity and auxin homeostasis in root development, its precise role remains unknown. Here, we provide experimental evidence that mitochondrial PDC E1 contributes to polar auxin transport during organ development. We performed genetic screens for factors involved in cotyledon development and identified a uncharacterized mutant, macchi-bou 1 (mab1). MAB1 encodes a mitochondrial PDC E1β subunit that can form both a homodimer and a heterodimer with IAR4. The mab1 mutation impaired MAB1 homodimerization, reduced the abundance of IAR4 and IAR4L, weakened PDC enzymatic activity, and diminished mitochondrial respiration. A metabolomics analysis showed significant changes in metabolites including amino acids in mab1 and, in particular, identified an accumulation of alanine. These results suggest that MAB1 is a component of the Arabidopsis mitochondrial PDC E1. Furthermore, in mab1 mutants and seedlings where the TCA cycle was pharmacologically blocked, we found reduced abundance of the PIN-FORMED (PIN) auxin efflux carriers, possibly due to impaired PIN recycling and enhanced PIN degradation in vacuoles. Therefore, we suggest that mab1 induces defective polar auxin transport via metabolic abnormalities.