Inulin-based prebiotics are non-digestible polysaccharides that influence the composition of the gut microbiota in infants and children, notably eliciting a bifidogenic effect with high short chain fatty acid levels. Inulin, a generic term that comprises β-(2,1)-linked linear fructans, is typically isolated from the chicory plant root, and derivatives such as oligofructose and long chain inulin appear to have different physiological properties. The first 1000 days of a child’s life are increasingly recognized as a critical timeframe for health also into adulthood, whereby nutri- tion plays a key role. There is an ever increasing association between nutrition and gut microbiota composition and development, with life health status of an individual. This review summarizes the latest knowledge in the in- fant gut microbiota from preterms to healthy newborns, as well as in malnourished children in developing coun- tries. The impact of inulin or mixtures thereof on infants, toddlers and young children with respect to intestinal function and immunity in general, is reviewed. Possible benefits of prebiotics to support the gut microbiome of malnourished infants and children, especially those with infections in the developing world, are considered, as well as for the pregnant mothers health. Importantly, novel insights in metabolic programming are covered, which are being increasing recognized for remarkable impact on long term offspring health, and eventual potential bene- ficial role of prebiotic inulins. Overall increasing findings prompt the potential for gut microbiota-based therapy to support health or prevent the development of certain diseases from conception to adulthood where inulin prebiotics may play a role.