A better knowledge of food system microbiomes will allow implementing a vast panel of smart microbiome modulators (SMMs), to be applied in integrative circular actions in smart microbiome food systems (SMFSs). Thanks to a better exploitation of strategic microbiome functionalities, SMFSs are more productive, safe, sustainable and resilient, being the gold standard for responsible, competitive and secure future EU food systems. Adequately and responsibly disseminated, the SMFPs, the food products derived from SMFSs, will join food quality and profound impacts in terms of sustainability and human health.