Patients with multiple chronic conditions, for example, musculoskeletal conditions and comorbidities, often receive inadequate and sometimes even contradictory care. Physiotherapists are well qualified to manage patients with musculoskeletal conditions and comorbidities due to their education and experience with rehabilitation; however, it is unknown which challenges they face when treating these patients. To identify challenges, treatment strategies, and delineations of areas of responsibility among physiotherapists working in private physiotherapy practice when treating people with musculoskeletal conditions and comorbidities. Qualitative study using focus group discussions and participant observations of 13 physiotherapists working in Danish private physiotherapy clinics. Grounded theory was applied to guide the analysis. Two major themes emerged from the focus groups and the observations (1) The necessity of adapting management to the patients and their treatment trajectory; (2) The dilemma of overall responsibility for coordinating care. The physiotherapists described different elements of adapting their management, including being challenged on time, taking extra care of the patient, and having to adjust to a fluctuating course of treatment. The dilemma in coordinating care concerned whether the responsibility should lie with the physiotherapist, other healthcare professionals, or the patients, and whether to treat only the condition on the referral or to treat all the conditions the patient had. Physiotherapists use adapted strategies for diagnosing and treating patients with musculoskeletal conditions and comorbidities and are uncertain about the overall responsibility for coordinating care and whether they should focus on the index condition alone or also the other comorbidities the patient has.