Chl, the central player in harvesting light energy for photosynthesis, is enzymatically degraded during natural turnover, leaf senescence, fruit ripening or following biotic/abiotic stress induction. The photodynamic properties of Chl and its metabolites call for tight regulation of the catabolic pathway enzymes to avoid accumulation of intermediate breakdown products. Chlorophyllase, the Chl dephytilation enzyme, was previously demonstrated to be an initiator of Chl breakdown when transcriptionally induced to be expressed during ethylene-induced citrus fruit color break or when heterologously expressed in different plant systems. Citrus chlorophyllase was previously shown to be translated as a precursor protein, which is subsequently post-translationally processed to a mature form. We demonstrate that maturation of citrus chlorophyllase involves dual N- and C-terminal processing which appear to be rate-limiting post-translational events when chlorophyllase expression levels are high. The chlorophyllase precursor and intermediate forms were shown to be of transient nature, while the mature form accumulates over time, suggesting that processing may be involved in post-translational regulation of enzyme in vivo function. This notion is further supported by the finding that neither N- nor C-terminal processed domains are essential for chloroplast targeting of the enzyme, and that both processing events occur within the chloroplast membranes. Studies on the processing of chlorophyllase versions truncated at the N- or C-termini or mutated to abolish C-terminal processing suggest that each of the processing events is independent. Dual N- and C-terminal processing, not involving an organellar targeting signal, has rarely been documented in plants and is unique for a plastid protein.