BackgroundThis study examines changes in physical functioning among adults aged 50-79 years in Germany based on data from two German National Health Interview and Examination Surveys conducted in 1997–1999 (GNHIES98) and 2008–2011 (DEGS1).MethodsUsing cross-sectional data from the two surveys (GNHIES98, n = 2884 and DEGS1, n = 3732), we examined changes in self-reported physical functioning scores (Short Form-36 physical functioning subscale (SF-36 PF)) by sex and age groups (50–64 and 65–79 years). Covariables included educational level, living alone, nine chronic diseases, polypharmacy (≥5 prescribed medicines), body mass index, sports activity, smoking and alcohol consumption. Multimorbidity was defined as ≥2 chronic diseases. Multivariable models were fitted to examine consistency of changes in physical functioning among certain subgroups and to assess changes in mean SF-36 PF scores, adjusting for changes in covariables between surveys.ResultsMean physical functioning increased among adults aged 50–79 years between surveys in unadjusted analyses, but this change was not as marked among men aged 65–79 years who experienced rising obesity (20.6 to 31.5%, p = 0.004) and diabetes (13.0 to 20.0%, p = 0.014). Prevalence of multimorbidity and polypharmacy use increased among men and women aged 65–79 years. In sex and age specific multivariable analyses, changes in physical functioning over time were consistent across subgroups. Gains in physical functioning were explained by improved education, lower body mass index and improved health-related behaviours (smoking, alcohol consumption, sports activity) in women, but less so among men.ConclusionsPhysical functioning improved in Germany among adults aged 50–79 years. Improvements in the population 65–79 years were less evident among men than women, despite increases in multimorbidity prevalence among both sexes. Changes in health behaviours over time differed between sexes and help explain variations in physical functioning. Targeted health behaviour interventions are indicated from this study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12877-016-0377-0) contains supplementary material, which is available to authorized users.