Animal-based proteins constitute a significant ingredient in European food systems. Dependence on animal-based proteins comes with substantial environmental and health impacts. Hence, the transition toward plant protein-based food systems is now more critical than ever. MICROBIOMES4SOY is an interdisciplinary and intersectoral project that employs a Multi-Actor Approach to ensure that food system actors' needs and key components relevant to the FOOD 2030 priorities are addressed. MICROBIOMES4SOY aims to enable transition pathways by delivering a comprehensive understanding of the microbiomes along the food and feed chains. Exploiting the microbiomes' full potential is essential to ensure sustainable and nutritious food and feed as they are important players throughout the food system, ranging from primary production, where microbes improve plant growth and health, to food production based on microbial processes and ultimately linking to the interactions between animal/human microbiomes and host health. MICROBIOMES4SOY focuses on the soya bean model system, an important protein-rich crop. The project will develop second-generation microbiome applications that sustain crop productivity and improve soya bean seeds' nutritional value and safety under different environmental conditions. MICROBIOMES4SOY will test the effect of dietary intervention based on soya bean-derived protein on the human gut microbiome and health and elaborate microbiome-informed dietary recommendations. The project will also employ microbiome-based solutions to develop novel aquafeeds and establish their effects on the fish gut microbiome and health. MICROBIOMES4SOY consortium comprises 19 partners from 11 countries contributing complementary expertise on soil, plant, human and animal microbiomes, bioinformatics, modelling, crop production, aquaculture, food/feed production, food systems mapping and scientific communication.