Background: Although midwives make clinical decisions that have an impact on the health and well-being of mothers and babies, little is known about how they make those decisions. Wide variation in intrapartum decisions to refer women to obstetrician-led care suggests that midwives' decisions are based on more than the evidence based medicine (EBM) model - i.e. clinical evidence, midwife's expertise, and woman's values - alone. With this study we aimed to explore the factors that influence clinical decision-making of midwives who work independently. Methods: We used a qualitative approach, conducting in-depth interviews with a purposive sample of 11 Dutch primary care midwives. Data collection took place between May and September 2015. The interviews were semi-structured, using written vignettes to solicit midwives' clinical decision-making processes (Think Aloud method). We performed thematic analysis on the transcripts. Results: We identified five themes that influenced clinical decision-making: the pregnant woman as a whole person, sources of knowledge, the midwife as a whole person, the collaboration between maternity care professionals, and the organisation of care. Regarding the midwife, her decisions were shaped not only by her experience, intuition, and personal circumstances, but also by her attitudes about physiology, woman-centredness, shared decision-making, and collaboration with other professionals. The nature of the local collaboration between maternity care professionals and locally-developed protocols dominated midwives' clinical decision-making. When midwives and obstetricians had different philosophies of care and different practice styles, their collaborative efforts were challenged. Conclusion: Midwives' clinical decision-making is a more varied and complex process than the EBM framework suggests. If midwives are to succeed in their role as promoters and protectors of physiological pregnancy and birth, they need to understand how clinical decisions in a multidisciplinary context are actually ...