Introduction Regular physical activity (PA) and good motor performance are essential for children's physical and mental health. However, historical trends suggest that levels of PA and motor performance in children and adolescents are at a low point. The relationships between PA, motor performance, health and their respective determinants, as well as their individual development throughout childhood and adolescence, are not yet fully understood. Therefore, continuous monitoring of PA, motor performance and health is needed to identify vulnerable subpopulations and provide data for policy-makers and health promotion professionals. The Motorik Monitoring 2.0-Study aims to analyse the developmental, historical and periodic trends in motor performance and PA, as well as the underlying determinants, in children and adolescents in Germany.Methods and analysis A representative sample of children and adolescents aged 4-17 years is drawn across 195 sample points in Germany. The assessment, carried out by test instructors, includes (1) a PA questionnaire covering different settings, including determinants, (2) anthropometric measures, (3) fine and gross motor performance tests focusing on coordination, flexibility, strength and endurance, (4) 24 hours device-based measured physical behaviour by accelerometry for 1 week and (5) a health interview focusing on health behaviour, physical and mental health as well as socioeconomic status. In addition, external data may be linked to the study using geographical information systems (eg, area deprivation, access to sports facilities). Analyses will be conducted using mixed-effects models to account for the nationwide structure of the study.Ethics and dissemination Ethical approval was obtained from the Ethics Committee of the Karlsruhe Institute of Technology. Results will be published in open-access scientific journals and disseminated at congresses for scientists, policy-makers and stakeholders.Trial registration number The study was registered in the NFDI4health database (https://csh.nfdi4health.de/resource/1034). The NFDI4health database is a central platform of the National Research Data Infrastructure for Personal Health Data. It is used to collect, manage and provide health data for scientific research and facilitates access to high-quality data for epidemiological and clinical studies.