Current efforts to reduce the incidence of non-communicable disease (NCD) are slow, but increasing evidence highlights the microbiome as a potential target for prevention. The majority of microbial development occurs in the first 1,000 days of life, presenting opportunities for strategic intervention to reduce the prevalence of future NCDs. In this review, we explore the social, structural, and political barriers that may hinder physiological gut microbial development in the first 1,000 days in the context of current scientific knowledge, focusing on nutritional factors in pregnancy, and during the exclusive breastfeeding and complementary feeding periods. We summarise emerging evidence and explore obstacles to nutritional choices affecting microbial development, and unpack the rhetoric that healthy eating to develop a microbiome that supports optimum health is an individual choice. As evidence on the role of the microbiome in health and disease grows, specific attention must be applied to existing social, structural, and political barriers that may hinder optimal microbial development. Addressing the role of corporate actors and social determinants influencing dietary choices and barriers surrounding breastfeeding must be prioritised, alongside efforts to advance basic scientific research. Until a wider public health perspective is taken, the success of interventions and recommendations will be limited.