Treatment in glutaryl-CoA dehydrogenase deficiency, an inborn error of metabolism of lysine and tryptophan, is mainly based on restriction of lysine intake, supplementation of carnitine, and an intensification of therapy during intercurrent illnesses. The major principle of dietary treatment is to reduce the production of glutaric acid and 3-hydroxyglutaric acid by restriction of natural protein in general and of lysine in particular. In parallel to development, the growing child learns to utilize different protein sources, shifting the primarily milk-based diet to a mixed diet. The changes in nutritional demands and food composition during the first years of life greatly influence nutritional support for affected patients at different ages. This article highlights frequent pitfalls of dietary treatment for this disease and focuses on particular risks of malnutrition in terms of essential amino acids and micronutrients and/or excess intake of lysine between age 3 months and age 6 years. We conclude from the examples given that restriction of natural protein intake plus application of lysine-free amino acid mixtures minimizes the risk of malnutrition and allows a reliable control of protein and lysine intake and, thus, seems particularly recommendable during the vulnerable period for acute encephalopathic crises. The efficacy of these theoretical and experience-based approaches to dietary treatment of glutaryl-CoA dehydrogenase deficiency should be investigated in detail in prospective clinical studies.