Detrimental metabolic programming has become a determinant factor in obesity propensity and the development of metabolic disorders; therefore, the search of nutritional strategies to reverse it is very relevant. Pectin is a prebiotic with health-promoting effects, such as control of glucose homeostasis and lipid metabolism, although other possible health effects and the prevention of obesity have been poorly studied. We studied the effects of chronic physiological supplementation with high-esterified pectin (HEP) in the reversion of metabolic nutrition-sensitive malprogramming associated with gestational undernutrition. As a model of nutrition-sensitive malprogramming, we used the progeny of rats with mild calorie restriction (CR) during pregnancy and analyzed their performance under metabolic stress (high-sucrose diet). We focused on the study of the sensitivity to the main adipostatic/adipokine hormones, i.e., leptin, insulin, and adiponectin, at both peripheral (liver and circulating parameters) and central (hypothalamus) levels. Our main findings suggest that chronic HEP supplementation is able to prevent weight/fat gain, to substantially reverse the detrimental malprogramming caused by the CR condition, to improve general health circulating markers, to modulate oxidative/lipogenic balance in the liver and energy metabolism regulators in the hypothalamus, and to restore/improve adipostatic/adipokine sensitivity affected by maternal calorie restriction, both peripherally and centrally. HEP stands out as a food component potentially useful against the development of metabolic disorders and obesity.