In this article, we examine the inter-relationship between moral theory and the unpredictable and complex world of primary health care, where the values of patient and doctor, or groups of patients and doctors, may often clash. We introduce complexity science and its relevance to primary care; going on to explore how it can assist in understanding ethical decision making, as well as considering implications for clinical practice. Throughout the article, we showcase aspects and key concepts using examples and a case study developed from our day-to-day experience working as clinical practitioners in primary care.