Protein–energy malnutrition promotes adaptive hormonal changes that result in stunting. A previous study showed that stunted children had increased insulin sensitivity and diminished pancreatic β-cell function. The objectives of the present study were to analyse the glucose, insulin, homeostasis model assessment of insulin sensitivity (HOMA-S) and homeostasis model assessment of pancreatic β-cell function (HOMA-B) levels after nutritional recovery. The recovered group (n 62) consisted of malnourished children after treatment at a nutrition rehabilitation centre. At the beginning of treatment their age was 2·41 (sd 1·28) and 2·31 (sd 1·08) years, weight-for-age Z score − 2·09 (sd 0·94) and − 2·05 (sd 0·55) and height-for-age Z score − 1·85 (sd 1·11) and − 1·56 (sd 0·90), for boys and girls respectively. The control group consisted of well-nourished children without treatment (n 26). After treatment, boys of the recovered group gained 1·29 (sd 1·06) Z scores of height-for-age and 1·14 (sd 0·99) Z scores of weight-for-age, and girls, 1·12 (sd 0·91) and 1·21 (sd 0·74) Z scores respectively. No differences were found between control and recovered groups in insulin levels for boys (P = 0·704) and girls (P = 0·408), HOMA-B for boys (P = 0·451) and girls (P = 0·330), and HOMA-S (P = 0·765) for boys and girls (P = 0·456) respectively. The present study shows that the changes observed previously in glucose metabolism and insulin were reverted in children who received adequate treatment at nutritional rehabilitation centres and showed linear catch-up.