IntroductionBecause patients with a “suspicion of Lyme borreliosis (LB)” may experience medical wandering and difficult care paths, often due to misinformation, multidisciplinary care centers were started all over Europe a few years ago. The aim of our study was to prospectively identify the factors associated with the acceptance of diagnosis and management satisfaction of patients, and to assess the concordance of the medical health assessment between physicians and patients 12 months after their management at our multidisciplinary center.MethodsWe included all adults who were admitted to the Tick-Borne Diseases Reference Center of Paris and the Northern Region (TBD-RC) (2017–2020). A telephone satisfaction survey was conducted 12 months after their first consultation. It consisted of 5 domains and 13 items rated between 0 (lowest) and 10 (highest grade): (1)Reception; (2)Care and quality of management; (3)Information/explanations given to the patients; (4)Current medical condition and acceptance of the final diagnosis; (5)Overall appreciation. Factors associated with diagnosis acceptance and management satisfaction at 12 months were identified using logistic regression models. The concordance of the health status as assessed by doctors and patients was calculated using a Cohen’s kappa test.ResultsOf the 569 patients who consulted, 349 (61.3%) answered the questionnaire. Overall appreciation had a median rating of 9 [8;10] and 280/349 (80.2%) accepted their diagnoses. Patients who were “very satisfied” with their care paths at TBD-RC (OR = 4.64;CI95%[1.52–14.16]) had higher odds of diagnosis acceptance. Well-delivered information was strongly associated with better satisfaction with the management (OR = 23.39;CI95%[3.52–155.54]). The concordance between patients and physicians to assess their health status 12 months after their management at TBD-RC was almost perfect in the groups of those with confirmed and possible LB (κ = 0.99), and moderate in the group with other diagnoses (κ = 0.43).ConclusionPatients seemed to approve of this multidisciplinary care organization for suspected LB. It helped them to accept their final diagnoses and enabled a high level of satisfaction with the information given by the doctors, confirming the importance of shared medical decisions, which may help to reduce health misinformation. This type of structure may be useful for any disease with a complex and controversial diagnosis.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-023-08352-3.