The efficiency of carbon and energy flows throughout metabolism defines the potential for growth and reproductive success of plants. Understanding the basis for metabolic efficiency requires relevant definitions of efficiency as well as measurements of biochemical functions through metabolism. Here insights into the basis of efficiency provided by 13C-based metabolic flux analysis (MFA) as well as the uses and limitations of efficiency in predictive flux balance analysis (FBA) are highlighted. 13C-MFA studies have revealed unusual features of central metabolism in developing green seeds for the efficient use of light to conserve carbon and identified metabolic inefficiencies in plant metabolism due to dissipation of ATP by substrate cycling. Constraints-based FBA has used efficiency to guide the prediction of the growth and actual internal flux distribution of plant systems. Comparisons in a few cases have been made between flux maps measured by 13C-based MFA and those predicted by FBA assuming one or more maximal efficiency parameters. These studies suggest that developing plant seeds and photoautotrophic microorganisms may indeed have patterns of metabolic flux that maximize efficiency. MFA and FBA are synergistic toolsets for uncovering and explaining the metabolic basis of efficiencies and inefficiencies in plant systems.