Zinc and vitamin A are essential micronutrients that influence intestinal health, metabolism, and overall physiology. Despite their essentiality, deficiencies in these nutrients are prevalent—especially in developing countries with plant-based diets. Additionally, the gap in knowledge of their interrelationship spans approximately 20 years. This dissertation delves into dietary zinc’s impact on vitamin A physiology and intestinal health parameters including small intestine morphology, functionality, and the gut microbiome, highlighting how different dietary sources affect nutrient interactions, absorption, and the gut microbiome, in vivo (G. gallus). An additional aim is to explore functional foods as a dietary source for gut health in vivo, and to evaluate a biofortification intervention to improve zinc uptake and status in a vulnerable Guatemalan population. Chapter 1 summarizes a review of literature whereby the essential roles of dietary zinc and vitamin A, their intestinal absorption and roles in intestinal health (brush border membrane tissue morphology, functionality, immunity, and the gut microbiome) in human and animal models are discussed. The current understanding of dietary zinc’s impact on vitamin A nutriture are highlighted, with a review of proposed mechanisms and research gaps. Chapter 2 evaluates the effects of zinc and vitamin A on intestinal functionality, morphology, and the gut microbiome, to provide novel insights and address current knowledge gaps. Chapter 3 explores varying levels of dietary zinc deficiency and the impacts on Zn physiological status, vitamin A physiology and metabolism, and intestinal morphology and functionality. Chapter 4 investigates the potential health benefits and functional properties of apple fractions in intestinal health and microbiome composition. Specifically, influence on essential trace mineral (iron and zinc) transporters to understand their role in mineral absorption and microbiome health. Chapter 5 explores soy-fortified bread as a practical food to improve iron absorption and intestinal health (brush border membrane morphology, functionality, and the gut microbiome), in vivo. In Chapter 6, the efficacy of zinc-, iron-, and protein-biofortified maize to improve zinc status among women and children in rural Guatemala is investigated. Finally, Chapter 7 reviews each chapter’s conclusions and outlines directions for future research.