Purpose We aimed to develop a modular Core Set based on the International Classification of Functioning, Disability and Health (ICF) for describing functioning in patients with substance use disorders (SUDs). To match the structure of the German health service system, the Core Set was split into modules for different service segments. Methods We followed a consensus process including several preparatory studies. To identify candidate ICF categories, we performed an ICF linking of guideline-recommended assessments, patient focus groups and patient and expert surveys. Categories were prioritized for different service segments and compiled into preliminary modules. The Core Set was tested in 13 treatment sites. Health professionals rated each category’s relevance, and contents of the Modular ICF-based Core Set for SUDs (MCSS) were compared to patient-reported treatment goals. An advisory board decided on revisions to the MCSS. Results The MCSS consists of a basic module (25 categories) and five additional modules for these treatment segments: counselling (8), qualified withdrawal (6), orientation (7), rehabilitation (32), and social integration services (10). Conclusions The MCSS provides a framework for harmonizing communication, documentation and interface management in German SUD health services. The basic module, consisting of 25 categories, can be employed as a Brief ICF Core Set. Implications for rehabilitation The MCSS can serve as a standard for describing functioning in patients with SUDs in Germany, as well as harmonize communication and reporting of treatment relevant information. In clinical practice, the MCSS can be used for the structured assessment of psychosocial problems and participation restrictions, goal setting, and outcome evaluation. Although the MCSS was developed in Germany, its proximity to the themes frequently identified in the literature regarding SUDs internationally suggests that it may be of use in other countries as well. The basic module may be employed as a Brief ICF Core Set.