26.03.2026

The gut microbiome is a transducer of the health effects of many food ingredients because of its ability to convert them into health-impacting compounds. Plant-forward diets and plant ingredients are recognized as health promoting, with recent added impetus provided by the drive to provide consumers with more sustainable protein sources than meat. Soy-based foods are good protein sources, and they contain a variety of other ingredients such as fibre that can impact the microbiome. This review explores the health benefits reported for soy-containing foods and the role of microbiome involvement in health effects. It describes the bi-directional relationship between dietary soy and the human gut microbiome whereby microbial metabolism transforms soy-derived compounds into bioactive forms that influence host physiology, while soy consumption shapes gut microbiota composition and activity. Factors modulating the health effects of soy such as fermentation, bioavailability, and consumers’ individual microbiome configurations are discussed. Current research limitations, including inconsistent methodologies and a lack of longitudinal dietary intervention studies are addressed, as well as the need for multiple omics approaches in microbiome research. Finally, we present an interdisciplinary perspective of the complexity of soy-microbiome interactions, potential for health promotion, and relationship to sustainability.