Chloroplast glutamyl endopeptidase (CGEP), a stromal S9D peptidase, was found to be a member of the peptidase network that governs chloroplast proteostasis. Using the PICS technique, CGEP was found to degrade proteins smaller than 25 kDa, cleaving the C-terminal of glutamate. Comparative proteomics showed that the null mutant (cgep) altered protein accumulation levels in starch metabolism, stromal protein folding machinery, and ribosomal proteins.