Activated fatty acid (fatty acyl CoA) can cross the outer membrane of mitochondria and enter the intermembrane space. Here, it undergoes another reaction.

With the help of an enzyme called carnitine acyl transferase I, the fatty acyl group is transferred onto a molecule called carnitine. This forms fatty acyl carnitine. Fatty acyl carnitine can cross the inner mitochondrial membrane with the help of an translocase enzyme and enter into the matrix.

Once inside the matrix, the carnitine is removed and a mitochondrial coenzyme A group is added back to the fatty acyl to re-form fatty acyl CoA. This reaction is catalysed by carnitine acyl transferase II. Fatty acyl CoA is now at the right location to undergo β-oxidation.

Carnitine acyl transferase I, is important because it is involved in the regulation of fatty acid breakdown (β-oxidation).

Carnitine acyl transferase I is regulated by an intermediate of the fatty acid synthesis pathway called malonyl CoA.