The large ATP synthase gene cluster of spinach chloroplasts is a multigenic cluster that encodes the small ribosomal subunit 2 followed by four ATP synthase subunits. The stoichiometry of the ATP synthase gene products from this cluster changes markedly between transcription and assembly of the complex. The two primary transcripts from this gene cluster undergo a complex series of RNA processing steps. Here we show that the extensive RNA processing that the large ATP synthase gene cluster transcripts undergo results in a substantial change in the stoichiometry of complete open reading frames (ORFs) of the four ATP synthase genes. Processing directly affects the stoichiometry of open reading frames from this gene cluster by intragenic cleavage. It may also affect open reading frame stoichiometry more indirectly, but equally significantly, by cleavage-induced alteration of stability of some of the processed transcripts relative to the others.