Dissection of organismal metabolomes into smaller subunits of life holds the potential to unravel the details of operative metabolic pathways and metabolic compartmentation at the sub-cellular level. Although metabolomes have been characterized at tissue, cellular, and cell-population types, little efforts have been put towards separation of sub-cellular metabolomes. Obvious challenges in lack of pure preparations of organelles, shared metabolites among them, and complicated metabolic regulations in them has impeded our advances in this domain of metabolomics. However, in the post-genomic era, significant advances have been made in predicting plant protein and transcriptomic localization to subcellular organelles through computational approaches. We summarize the recent efforts and progresses made in directions of understanding the plant sub-cellular (organellar) metabolomes.