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Background In outpatient care in Germany, medical assistants (MAs) are the contact persons for patients’ concerns and their working conditions are relevant to their own health and the provided quality of care. MAs working conditions have been described as precarious leading to high levels of work stress. Consequently, we aimed to examine MAs’ needs for work-related improvements. Methods We surveyed 887 employed MAs between September 2016 and April 2017. A 20-item questionnaire measured desired improvements. To measure correlations between variables we computed a matrix of tetrachoric correlations for binary variables and performed an exploratory factor analysis. We ran ordinal logistic regression models employing 11 independent variables to examine determinants of needs. Results A total of 97.3% of the participants expressed any need and, on average, 10.27 needs were reported. Most frequently, needs were expressed related to a higher salary (87.0%), less documentation (76.0%) and more recognition from society (75.4%). Exploratory factor analysis suggested three dimensions of needs for work-related improvements (i.e. working conditions, reward from the supervisor and task-related independence). Ordinal logistic regression models only identified determinants for the outcome variable task-related independence, which was more frequent in those with longer work experience or in a leadership position. Conclusions The high prevalence of desired workplace-related improvements among MAs highlights the relevance of modifying their working conditions. The fact that we found only few determinants signals that there are no specific high-risk subgroups, but interventions to improve MAs’ working conditions should target the entire MA population. Electronic supplementary material The online version of this article (10.1186/s12995-019-0237-x) contains supplementary material, which is available to authorized users.