The co-existence of different types of medical systems (medical pluralism) is a typical feature of India's healthcare system. For conditions such as influenza-like illness (ILI), where non-specific disease signs/symptoms exist, clinical reasoning in the context of medical pluralism becomes crucial. Recognising this need, we undertook a qualitative study, which explored factors underpinning clinical decisions on diagnosis and management of ILI. The study involved semi-structured interviews including clinical vignettes with 20 healthcare practitioners (working within allopathy, homeopathy and Ayurveda) working in the private healthcare sector in Solapur city, India. An inquiry was conducted into criteria influencing the diagnosis, treatment, referral to specialist care and role of treatment guidelines for ILI. Thematic analysis was used to identify aspects relating to ILI diagnosis, treatment and referral. The diagnosis of influenza was based largely on clinical symptoms suggestive of influenza in the absence of other diagnoses. Referral for laboratory tests was only initiated if illness did not resolve, generally after 2-3 consultations. Antibiotics were often prescribed for persistent illness, with antivirals rarely considered. Some differences between practitioners from different medical systems were observed in relation to treatment and referral in case of persistent illness. A combination of analytical and intuitive clinical reasoning was used by the participants and clinical decisions were based on both social and clinical factors. Clinical decision-making was rarely a linear process and respondents felt that broad guidelines on influenza that allowed doctors to account for the sociocultural context within which they practised medicine would be helpful.