Objectives Pharmacy risk factors impose a major threat to general healthcare outcomes. Risks that can directly affect patients are known as clinical risk factors, and other, non-clinical risk factors may also affect a pharmacist's performance and pharmaceutical profession. This study aims to evaluate the risks, which occur in community pharmacies in Abu Dhabi, and to investigate the protective plans followed in such incidence. Methods A self-administrated online questionnaire was distributed to community pharmacists in Abu Dhabi. The questionnaire items were tested by content and face validity in a panel of experts and pilot study. The Statistical Package for the Social Sciences (SPSS) program was used for the data analysis. Key findings Medication errors and computer system malfunction occur monthly, as reported by 40% of the participants (n = 131). Theft cases were reported by 37.6% (n = 121) of the pharmacists. Violence was categorized as verbal, psychological and physical abuse, and the frequency was 56.8% (n = 183), 30.4% (n = 98) and 14.3% (n = 46) respectively. Almost all the participants belief that communication skills, alertness and experience are the most important internal factors affecting performance. Environmental factors such as the availability of restrooms were cited as important external factors enhancing performance. Chain pharmacies were found to address electrical failure and dealing with look-alike sound-alike/high-alert medication efficiently. Conclusions Different types of clinical and non-clinical risk in pharmacy practice were identified, and risk mitigation techniques were proposed. A positive attitude of community pharmacists was observed towards identifies risks and on the suggested mitigation techniques. It is necessary to publish a universally referenced validated risk factor list for evaluating current risk management plans to maintain safe pharmacy practices and include management courses within pharmacy curriculum.