Introduction Approximately one in five workers in Europe is engaged in shift work. Studies reveal that night shift work leads to an increased risk of overweight, obesity and related diseases. Yet, the biological and behavioural mechanisms underlying these associations are not fully understood. The cross-sectional and mechanistic studies within the European SHIFT2HEALTH project aim to investigate biological, behavioural and psychosocial key risk factors responsible for the association between night work and obesity across five European countries. Methods A multi-centric cross-sectional study is designed to unravel obesogenic risk factors, eating habits and sleep patterns in night shift workers and day workers from the health- and various industrial sectors. Recruitment takes place in Austria, Denmark, Germany, Poland, and the Netherlands, aiming at 500 night shift workers and 500 day workers. Anthropometric measurements, sensory perception and food preference tests are performed, alongside extensive questionnaires. In addition, biological samples (blood, hair, urine, faeces) are collected for biomarker measurements of inflammation, oxidative stress, glycaemic and lipaemic parameters, for microbiome and metabolomics analyses and chronotype assessment. In a nested mechanistic study, night shift workers (N=200) recruited in Austria and in the Netherlands, additionally collect urine samples from all voids over 24 hours during a day shift and a night shift, as well as dried blood spots and tongue swabs at four time points and undergo continuous sleep, activity and light exposure monitoring through actigraphy. The association between night shift work and its metrics with levels of pre-obesity biomarkers will be evaluated in crude and multivariable-adjusted regression models, adjusting for potential confounders. Stratified analyses by age, gender, sector and chronotype will be conducted. Conclusion In the cross-sectional and mechanistic studies of the SHIFT2HEALTH project, biological, behavioural and psychosocial factors of night shift workers will be compared with those of day workers across sectors. The outcomes of these studies will serve as a basis for future intervention studies and, together, will contribute to the development of strategies to prevent and reduce overweight and obesity with the aim to improve the health and wellbeing of night shift workers. Trial registration: clinicaltrials.gov, ID: NCT06288568.