Abstract Background Little is known about the management of methicillin-resistant Staphylococcus aureus (MRSA) carriers in the German outpatient sector and about the impact of MRSA on their daily life. Reimbursement for MRSA related costs in the German outpatient sector is available since 2012, but its impact has not been studied yet. The aim of the study was to analyze the outpatient management of MRSA carriers from both, physicians’ and MRSA carriers’ perspective. Methods Paper-based questionnaires were mailed to physicians providing outpatient care and to MRSA carriers in 2013. MRSA carriers were recruited among patients tested positive for MRSA during a hospital stay in 2012. General practitioners, specialists for internal medicine, urologists, and dermatologists working in the outpatient catchment areas of the hospitals were contacted. Results Out of 910 MRSA carriers 16.5 % completed the questionnaires; among 851 physicians 9.5 % participated. 27.3 % of the responding MRSA carriers stated that no healthcare professional had ever talked to them about MRSA. 17.4 % reported self-stigmatization in terms of restricting social contacts; 47.3 % remembered decolonization and 33.3 % reported that their MRSA status was checked after discharge. Physicians displayed heterogeneous attitude and activity towards MRSA (number of applied decolonization and MRSA screenings). A minority (15.2 %) were satisfied with the reimbursement of costs, 35.9 % reported full agreement with the general recommendations for the handling of MRSA carriers. Conclusions MRSA carriers appear not well informed; (self-) stigmatization is occurring and should be tackled. Greater awareness of MRSA as a problem in the outpatient sector could lead to a better handling of MRSA carriers.