Driven by the concept of "We Are What We Build," the institute was designed using food-based materials. The materials selected were vetted through a matrix that compared factors of health, sustainability and connection to food. This process helped to locate materials that responded to each factor while eliminating those that did not. For example, milk-based paint was initially selected, but ultimately dismissed due to concerns for lactose intolerance. The linoleum flooring contains materials from flax and jute plants. The pantry area utilizes wheat-board while other millwork includes the use of solid palmwood in the staff support areas. The design reflects the notion that while access to an unlimited range of food is something often taken for granted, for a certain population, interaction with food presents a continual challenge and identification of food is paramount.

Food-based materials are integrated with a more perceptible food image-based system of wayfinding. The two approaches work in tandem to support a creative and succinct architectural expression. Instead of typical door numbers, the rooms are identified by everyday objects carved into the doors such as clocks, baseballs and buttons. This detail makes the clinical experience more stimulating for children and more fun for them to locate their rooms.

Special food challenge rooms are designed to test patients' allergic reactions. In the main circulation/information spine, wall-to-ceiling panels displaying vivid, abstract images of fruit create a positive environment that reminds patients of the beauty of food. Appropriately designed, the Jaffe Food Allergy Institute at Mount Sinai Hospital encourages children to not be afraid of experiencing new foods.