ATP‐binding cassette (ABC) subfamily D transporters are important for the uptake of fatty acids and other beta‐oxidation substrates into peroxisomes. Genetic and biochemical evidence indicates that the transporters accept fatty acyl‐coenzyme A that is cleaved during the transport cycle and then re‐esterified in the peroxisomal lumen. However, it is not known whether free coenzyme A (CoA) is released inside or outside the peroxisome. Here we have used Saccharomyces cerevisiae and isolated peroxisomes to demonstrate that free CoA is released in the peroxisomal lumen. Thus, ABC subfamily D transporter provide an import pathway for free CoA that controls peroxisomal CoA homeostasis and tunes metabolism according to the cell’s demands.