The Ketogenic Diet (KD) is a non-pharmacological strategy for drug-resistant epilepsy (DRE) and inborn errors of metabolism (Glut-1 deficiency) management. KD is characterized by being restrictive, affecting micronutrient intake. There are different modalities of KD in which food intake and nutritional deficiencies vary. Objective: To determine the micronutrient intake in different KD modalities. Patients and Method: Observational, cross-sectional study with patients diagnosed with DRE and Glut-1 deficiency. The dietary intake of 21 micronutrients was evaluated, and analyzed according to KD modality [Classic, Modified Atkins Diet (MAD)], use of special formula, and adequacy of recommended dietary intake (RDI) according to age and sex, defining < 75% as deficient. Results: 19 patients were evaluated, median age 62 months (IQR: 20.5-79), 12/19 (63.2%) male, 13/19 (68.4%) eutrophic, 5/19 (26.3%) gastrostomy users, 10 (52.6%) MAD modality, use of special formula 7/19 (36.8%). Micronutrient deficiencies were found in 16/21 (76.2%) in the classic diet and 9/16 (42.9%) in the MAD. The intake of vitamin D, B2, B12, sodium, phosphorus, zinc, and selenium was significantly lower in the classic diet than in DMA, the median intake adequacy of vitamins A, C, D, E, and K was > 100%. The use of special formula manages to complete the requirements in MAD. Conclusions: The micronutrient intake in the different KD modalities is low for most of them, being the MAD with formula the one that presented a more adequate micronutrient intake. These results should be considered in nutritional follow-up and supplementation planning.