This review offers an overview of the current state of our knowledge concerning the role of fructose-1,6-bisphosphatase (FBPase) in sugar partitioning and biosynthesis, through the analysis of genetically manipulated plants. The existence of two well-characterized isoforms is a consequence of the subcellular compartmentalization of photosynthetic eukaryotes, conditioning their respective regulatory mechanisms and their influence over plant metabolism and photosynthesis. Both isoforms are important, as has been deduced from previous work with different plant species, although there is still much to be done in order to gain a definitive vision of this issue. Despite that, alteration of the FBPase content follows a general pattern, there are some differences that could be considered species-specific. Modifications lead to profound changes in the carbohydrate content and carbon allocation, raising questions as to whether flux of some sugars or sugar precursors from one side to the other of the chloroplast envelope occurs to rebalance carbohydrate metabolism or whether other compensatory, though not fully efficient, enzymatic activities come into play. Due to the pleiotropic nature of modifying the core carbon metabolism, an answer to the above questions would require an exhaustive study involving diverse aspects of plant physiology.