Abstract Background Antibiotics are over-prescribed for upper respiratory tract infection (URTI). It is unclear how factors known to influence prescribing decisions operate ‘in the moment’: dual process theories, which propose two systems of thought (‘automatic’ and ‘analytical’), may inform this. Objective(s) Investigate cognitive processes underlying antibiotic prescribing for URTI and the factors associated with inappropriate prescribing. Methods We conducted a mixed methods study. Primary care physicians in Scotland (n = 158) made prescribing decisions for patient scenarios describing sore throat or otitis media delivered online. Decision difficulty and decision time were recorded. Decisions were categorized as appropriate or inappropriate based on clinical guidelines. Regression analyses explored relationships between scenario and physician characteristics and decision difficulty, time and appropriateness. A subgroup (n = 5) verbalized their thoughts (think aloud) whilst making decisions for a subset of scenarios. Interviews were analysed inductively. Results Illness duration of 4+ days was associated with greater difficulty. Inappropriate prescribing was associated with clinical factors suggesting viral cause and with patient preference against antibiotics. In interviews, physicians made appropriate decisions quickly for easier cases, with little deliberation, reflecting automatic-type processes. For more difficult cases, physicians deliberated over information in some instances, but not in others, with inappropriate prescribing occurring in both instances. Some interpretations of illness duration and unilateral ear examination findings (for otitis media) were associated with inappropriate prescribing. Conclusion Both automatic and analytical processes may lead to inappropriate prescribing. Interventions to support appropriate prescribing may benefit from targeting interpretation of illness duration and otitis media ear exam findings and facilitating appropriate use of both modes of thinking.