Catalyzes the transfer of a malonyl moiety from malonyl-CoA to the free thiol group of the phosphopantetheine arm of the mitochondrial ACP protein (NDUFAB1). This suggests the existence of the biosynthesis of fatty acids in mitochondria. holo-[ACP] + malonyl-CoA = CoA + malonyl-[ACP] Lipid metabolism; fatty acid biosynthesis. Belongs to the type II malonyltransferase family.