Inadequate energy intake and poor diet quality are important causes of chronic child undernutrition. Strategies for improving diet quality using lipid-based nutrient supplements (LNS) are currently being tested in several countries. To date, information on children's dietary intakes during LNS use is available only from Africa. In this study, we collected 24-h dietary recalls at baseline, 3, 6, 9 and 12 months on Honduran children (n = 298) participating in a cluster-randomised trial of LNS. Generalised estimating equations were used to examine differences in number of servings of 12 food groups in the LNS and control arms, and multi-level mixed effects models were used to compare macro- and micronutrient intakes. Models accounted for clustering and adjusted for child's age, season and breastfeeding status. Mean daily servings of 12 food groups did not differ by study arm at baseline and remained similar throughout the study with the exception of groups that were partially or entirely supplied by LNS (nuts and nut butters, fats, and sweets). Baseline intakes of energy, fat, carbohydrates, protein, folate and vitamin A, but not vitamin B12, iron and zinc were lower in the LNS than control arm. The change in all macro- and micronutrients from baseline to each study visit was larger for the LNS arm than the control, except for carbohydrates from baseline to 9 months. These findings indicate that LNS improved the macro- and micronutrient intakes of young non-malnourished Honduran children without replacing other foods in their diet.