The prevalence of the double burden of malnutrition in society is well known with the coexistence of undernutrition with an increase in overweight/obesity; this has been increasing globally with nutritional imbalances and infectious diseases being the major etiological factors. However, there is also the coexistence of inappropriate adiposity or metabolic dysfunction in an individual who appears currently undernourished by anthropometric standards (stunted or underweight); this is the intraindividual double burden of malnutrition. It could also occur in temporal sequence, as anthropometric overweight in an individual who has previously endured childhood under-nutrition. IIDBM has increased the risk for diet-related non-communicable diseases over the past few decades, as it tracks into adulthood, warranting an urgent need for intervention and prevention. While gut dysbiosis has been associated with various forms of malnutrition, the early life gut microbiome composition and its related metabolites and regulatory factors, are possibly linked to the development of inflammatory and metabolic conditions in IIDBM. The possible underlying physiological mechanisms are reviewed here, working through host dietary influences, gut microbial metabolites, host inflammation and metabolic dysregulation. When validated experimentally and tested through appropriately designed randomised, controlled trials, these mechanistic insights will likely lead to development of preventive strategies.