Abstract Background The functional exposome approach examines the relationship between biological effects (internal exposome) and the sum of environmental exposures (external exposome). Multiple sclerosis (MS) is characterized by selective demyelination and acute inflammation; miRNAs and microbiota are emerging in the pathogenesis as inflammation and oxidative stress biomarkers. The EXPOSITION study protocol has been designed to study such biomarkers variation in response to the external exposome (air pollution, urbanization, lifestyles) in people with MS (pwMS). Methods EXPOSITION is a cross-sectional observational study collecting a sample of 200 pwMS residing in Lombardy, Northern Italy. Sample size is based on the prediction of differential expression of candidate miRNAs through bioinformatic analyses. All participants will be investigated for social, demographic and clinical data as well as general and specific external exposome factors. The internal exposome factors will be collected for each participant from blood and stool samples, as well as from nasal swabs. Exposome clustering and correlation statistical techniques will be applied and variation of miRNA and microbiota will be tested in association with the variation of the external exposome in urban and extra-urban environments. Results and conclusions The expected results will help pwMS and researchers understanding which biomarkers and which components of the external exposome are associated to oxidative stress and inflammation, to improve precision medicine and contrast disease progression. The relationship between urban exposome and biodiversity is an important dimension in the study of environmental impact on human health. This study may provide preliminary data to assess which nature-based solutions are suitable for enhancing the biodiversity of urban areas. Key messages • The functional exposome approach could be used to link environmental risk factors and disease biomarkers using the right methology. • EXPOSITION will quantify the variation of miRNA and microbiota in association with the variation of external exposome, in urban and extra-urban environments.