Nutrition interventions have an effect on growth, energy and nutrient intake, and development, but there are mixed reports on the effect of supplementation of energy-dense foods on dietary intake. This substudy aimed at assessing the effect of supplementation with corn–soy blend (CSB) or lipid-based nutrient supplement (LNS) on energy and nutrient intake in moderately underweight children participating in a clinical trial. A total of 188 children aged 8–18 months participated and received daily either 284 kcal from CSB or 220 kcal from LNS and no supplements (control). An interactive 24-h recall method was used to estimate energy and nutrient intakes in the groups. Total mean energy intake was 548 kcal, 551 kcal and 692 kcal in the control, CSB and LNS groups, respectively (P = 0.011). The mean (95% confidence interval) intake of energy and protein were 144 (37–250; P < 0.001) and 46 (1.5–7.6; P < 0.001) larger, respectively, in the LNS group than among the controls. No significant differences were observed between the control and CSB groups. Energy intake from non-supplement foods was significantly lower in the CSB group compared with the control group, but not in the LNS group, suggesting a lower displacement of non-supplement foods with LNS. Both CSB and LNS supplementation resulted in higher intakes of calcium, iron, zinc and vitamin C compared with controls (all P ≤ 0.001). This study indicates that LNS might be superior to CSB to supplement underweight children as it results in higher energy intake, but this requires confirmation in other settings.