The increasing role of three-dimensional (3D) cellular technology across the board in food and health science is continuously expanding to provide more in-depth and concise data to investigate functional food and pharmaceutical components in uptake, transport, and metabolism to provide easily comparable responses in both preliminary studies to later human trials. Organoids have been widely adopted in pharmaceutical studies, yet few functional food studies have followed the same approach. The traditionally used Caco-2 cell line provides an efficient preliminary response to functional foods. However, using 3D models allows an expanded array of testing, including incorporating disease-causing mutations to model disorders impacting nutrition uptake and metabolism, such as Crohn's disease. Here, we summarize current 3D cell systems available for food research and recent studies employing these models and highlight limitations as well as possible future strategies for the wider use of organoids in food research.