The growing body of research on human gut microbiota has revealed its crucial role in regulating numerous physiological processes, including digestion, immunity, and even mental health (Kau et al. Nature 474(7351):327–336, 2011). Understanding how individual microbiota profiles interact with dietary components has opened new avenues in personalized nutrition, enabling the design of individually tailored diets to improve health outcomes and prevent diseases (Johnson et al. Cell Host Microbe 25(6):789–802.e5, 2019). This chapter explores how the microbiome, through the production of key metabolites, can be modulated by diet to positively influence health (Sonnenburg and Bäckhed, Nature 535(7610):56–64, 2016). Improvements in the available food composition tables and advancements in microbiome-sequencing technologies, such as 16S rRNA gene sequencing and metagenomics (Lloyd-Price et al. Nature 569(7758):655–662, 2019), along with computational models, have made it possible to customize dietary recommendations, considering each individual’s unique microbiome composition (Heinken et al. Nat Biotechnol 41(9):1320–1331, 2023). We will discuss how the Stance4Health project has addressed this challenge by developing the “microbiota scores” algorithm, a tool that evaluates and ranks foods according to their capacity to nourish the microbiota in a healthy manner (Hinojosa-Nogueira et al. Nutrients 15(2):276, 2023) and that is integrated into the personalized dietary recommendation system of the i-Diet S4H app. This system facilitates the creation of personalized menus that not only meet nutritional requirements but also promote a favorable and sustainable intestinal environment in the long term (Dello Russo et al. Foods 11(10):1480, 2022). By integrating microbiota data into dietary recommendations, we can advance toward truly personalized nutrition, offering tailored interventions that enhance an individual’s metabolic, immune, and neurological health (Valdes et al. BMJ:k2179, 2018).