We report the significant increase of the content of free amino acids in Nicotiana benthamiana by the co-suppression of the ClpC1 and ClpC2 genes, which are translated to be the chaperonic part in the Clp protease at plastids. Clp protease with ClpC1 and ClpC2 proteins as the chaperonic part degrades denatured or improperly folded protein in plastids. Nicotiana benthamiana ClpC1 and ClpC2 genes (NbClpC1 and NbClpC2: NbClpC1/C2) share 93% similarities; therefore, co-suppression of the NbClpC1/C2 was possible using a single virus-induced silencing vector. Co-suppression of NbClpC1/C2 resulted in a pleiotropic phenotype including disappearance of apical dominance and formation of chlorotic leaves. NbClpC1/C2 co-suppressed leaves accumulated 11.9-fold more free amino acids than the GFP-silenced leaves. The co-suppression of NbClpC1/C2 did not change the expression levels of some selected genes in the biosynthetic pathways for the free amino acids, but reduced the total protein amounts to 32.5%, indicating that co-suppression affected the incorporation of free amino acids in proteins during translation. The loosely packed mesophyll cells and abnormal vascular bundles in the leaves suggested structural problems associated with translocation of free amino acids to sink tissues. NbClpC1/C2 co-suppression can offer a novel strategy for accumulation of free amino acids though it results in stunted growth.