Summary The distribution of essential metal ions over subcellular compartments for use as cofactors requires control of membrane transporters. PAA2/HMA8 is a copper‐transporting P1B‐type ATPase in the thylakoid membrane, required for the maturation of plastocyanin. When copper is highly available to the plant this transporter is degraded, which implies the action of a protease. In order to identify the proteolytic machinery responsible for PAA2/HMA8 turnover in Arabidopsis, mutant lines defective in five different chloroplast protease systems were analyzed. Plants defective in the chloroplast caseinolytic protease (Clp) system were specifically impaired in PAA2/HMA8 protein turnover on media containing elevated copper concentrations. However, the abundance of a core Clp component was not directly affected by copper. Furthermore, the expression and activity of both cytosolic and chloroplast‐localized superoxide dismutases (SODs), which are known to be dependent on copper, were not altered in the clp mutants, indicating that the loss of PAA2/HMA8 turnover in these lines was not caused by a lack of stromal copper. The results suggest that copper excess in the stroma triggers selection of the thylakoid‐localized PAA2 transporter for degradation by the Clp protease, but not several other chloroplast proteases, and support a novel role for this proteolytic system in cellular copper homeostasis.