Alternatives to cow's milk and soy milk are often necessary for children with food allergies. Although hydrolyzed and elemental formulas are appropriate replacements, other milk products such as rice and almond milk are insufficient protein sources for children under 2 years of age. A chart review on three patients treated for protein malnutrition in association with multiple diagnosed food allergies that resulted in refractory eczema revealed adverse outcomes that resulted from elimination diets. The use of rice milk resulted in hypoalbuminemia and poor weight gain in all cases, and multiple secondary infections in one patient. These cases illustrate the need for careful nutritional guidance in the management of food allergy, as well as the importance of cautious use and interpretation of testing for food allergies in the absence of a clear clinical history of reaction.