Background Low health literacy has important consequences for health status, medication adherence and use of health services. There is little insight from the perspective of pharmacy staff into how they identify the information needs of consumers and particularly the signals and risk factors of limited health literacy that they encounter in their day‐to‐day communication with consumers. Objective To investigate factors impacting on consumer health literacy, from the perspective of pharmacy staff. Methods The research comprised semi‐structured interviews conducted in a convenience sample of pharmacies in the south‐east region of Queensland, Australia. Eleven pharmacists and nine pharmacy assistants agreed to participate. Interviews were audio‐recorded and transcribed verbatim. Initial coding of the anonymized transcripts was performed using NVivo®. Codes were analysed into overarching themes and subthemes, which were then re‐named and refined through consensus discussion. Results Three overarching themes were identified from the coding process: complexity of the health system, clarity of information, and dialogue among consumers and health‐care professionals. Two of the themes were system related, namely the health system and pharmacy labels; the health literacy issues included lack of clarity, complexity and misunderstanding. The third theme was related to communication. Conclusions Complexity of the health system, clarity of information and dialogue among consumers and health‐care professionals were identified as factors associated with consumers' health literacy. We call for increased engagement between pharmacy staff and consumers with improved focus on areas of potential confusion, such as medicine labels and navigation of the health system, aiming to minimize negative consequences of limited health literacy and optimize patient health outcomes.