In 2015, the World Health Assembly called for ending all forms of malnutrition by 2030. The six major areas have been identified to accelerate the intervention programs. The areas focus on the reduction in stunting, anemia, wasting, low birth weight, and overweight, and the promotion of exclusive breastfeeding. Country like India is facing the dual burden of malnutrition, yet anemia and stunting are the major bottlenecks of India’s public health nutrition concerns. The micronutrient deficiencies are a significant contributor to the anemia and stunting. Although the causes of anemia and stunting are multifactorial, iron and zinc are crucial trace elements associated with the problems. India has been rolling out multiple prophylaxis programs since independence, but the success rate could be more optimal. The physiological system nicely orchestrates the homeostatic regulation of iron and zinc. Non-digested oligosaccharides and live microorganisms, i.e., prebiotics and probiotics, respectively, are essential in human nutrition and in understanding the complex absorption kinetics of iron and zinc. The chapter briefly introduces prebiotics and probiotics, and elucidates the intricate mechanisms of the impact of prebiotics and probiotics on the colonocytes and enterocytes to regulate the absorption of the elements, iron and zinc