Management plans for conservation and sustainable use of Moringa peregrina trees are needed to overcome overexploitation coupled with climate change effects. We examined the relationship between the stored energy and the persistence of the species. We conducted field, greenhouse, and lab experiments; at the levels of population cohorts, plant organs, seeds, and seedlings, to demonstrate the relationship between energy content and the persistence potential of the species. Seedlings and juveniles stored around 12,000 joule/g in roots, while uncoppiced adults stored about 9,000 joule/g in stems, and coppiced adults stored 1,800-4,000 joule/g in lignotubers. In adult trees, the number of sprouting stems is correlated with the energy content in lignotubers. Over the ten years of seed storage, a rapid rate of energy depletion was observed ranging from 16,821 to 5,059 joule/g, which is associated with decreased germination and viability. The amount of energy content in two-month-old seedlings varied from 240,000, to 800,000 joule/seedlings under 200 and 800 mm rainfall respectively. We reported an unstable population structure that could be ascribed to the depletion of stored energy in lignotubers following uncontrolled coppicing, and the rapid depletion of seed energy which hinders the persistence of M. peregrina populations.