Diet quality is a modifiable factor that may contribute to the onset of diet-related chronic diseases. Currently, in Spain there are no studies that examine the intakes and sources for total carbohydrates, starch, total sugar, and fiber by both children consuming all kind of milks and children regularly consuming adapted milk formulas. Our goal was to evaluate the contribution of different food groups to total carbohydrates, starch, total sugar, and fiber consumption within the EsNuPI study participants by assessing their usual intakes by applying two 24 h dietary recalls that were completed by 1448 children (1 to <10 years) divided into two cohorts: one Spanish Reference Cohort (SRS) of the general population (n = 707) and another cohort which included children consuming adapted milks including follow-on milk, toddler’s or growing up milk, fortified and enriched milks, here called Adapted Milk Consumers Cohort” (AMS) (n = 741). Estimation of the usual intake showed that nutrient intake increased with age for all nutrients except for fiber. The percentage of children by age and gender who met the reference intake (RI) range for total carbohydrates, was in all groups more than 50% of individuals, except for girls aged 6 to <10 years from the reference cohort in which only 46.9% complied the RI. Median fiber intake, both in the SRS and the AMS, was well below the adequate intake (AI) for children between 3 and 10 years. Main total carbohydrates sources were cereals, followed by milk and dairy products, fruits, bakery and pastry, vegetables and sugars and sweets. The highest contributors to starch intakes were cereals, bakery and pastry, vegetables, and fruits. Major sources of total sugar intakes were milk and dairy products, fruits, bakery and pastry, sugars and sweets, vegetables, and cereals. Nonetheless, milk and dairy products, and fruits, mainly provided lactose and fructose, respectively, which are not considered free sugars. Higher contribution to fiber intakes was provided by fruits, cereals, vegetables and bakery and pastry. There were no significant differences in relation with the total sugar intake according to the body mass index (BMI) between SRS and AMS. The present study suggests a high proportion of children had total carbohydrates intakes in line with recommendations by public health authorities, but still a significant number presented insufficient total carbohydrate and fiber intakes, while total sugar consumption was high, with no major differences between SRS and AMS cohorts.