Background: Clinical decision-making (CDM) is the dynamic process used to gather, interpret and evaluate data to select an evidence-based choice of action. As the role of the pharmacist becomes more patient-focused, effective CDM skills are increasingly vital to achieve patient outcomes centred on quality, safety and efficacy. Objective: To examine how community pharmacists reason through a clinical problem and what factors assist or hinder decision-making. Method: Fifteen New Zealand registered community pharmacists in central Auckland were presented with a bacterial conjunctivitis case. Think Aloud and protocol analysis were employed to examine pharmacists' cognitive processes when working through the case. Factors that affect CDM were explored through semi-structured interviews and analyzed using thematic analysis. Results: Pharmacists used pattern recognition and analytical reasoning to diagnose and recommend treatment. Three main factors affecting CDM were: 1. community pharmacy environment, where pharmacy size and layout prevented patient privacy; 2. clinical knowledge, which was outdated and limited by poor access to up-to-date resources; and 3. patient factors, where CDM was affected by time, patient's attitudes, and language barriers. When uncertain, pharmacists typically referred patients to their GP to ensure patient safety and believed offering treatment was not within their scope of practice. Conclusion: Pharmacists used dual processing when encountering a familiar case. Further research is required to explore how pharmacists apply CDM when exposed to less familiar, more complex cases presenting greater ambiguity. Barriers in community pharmacy deter effective CDM skills and could inhibit community pharmacists from fulfilling their expanding role within the modern healthcare system.