The inner mitochondrial membrane is impermeable to acetyl-CoA, so an indirect shuttle transfers acetyl group equivalents across the membrane. Intramitochondrial acetyl-CoA first reacts with oxaloacetate to form citrate, in the citric acid cycle reaction catalyzed by citrate synthase.

Citrate then passes through the inner membrane on the citrate transporter. In the cytosol, citrate cleavage by citrate lyase regenerates acetyl-CoA and oxaloacetate in an ATP-dependent reaction.

Oxaloacetate cannot return to the mitochondrial matrix directly, as there is no oxaloacetate transporter. Instead, cytosolic malate dehydrogenase reduces the oxaloacetate to malate, which can return to the mitochondrial matrix on the malate–α-ketoglutarate transporter, in exchange for citrate.

In the matrix, malate is reoxidized to oxaloacetate to complete the shuttle. However, most of the malate produced in the cytosol is used to generate cytosolic NADPH through the activity of malic enzyme. The pyruvate produced is transported into the mitochondria by the pyruvate transporter, then converted back into oxaloacetate by pyruvate carboxylase in the matrix.