Abstract Background Home births in high risk pregnancies and unassisted childbirth seem to be increasing in the Netherlands. Until now there were no qualitative data on women’s motivations for these choices in the Dutch maternity care system where integrated midwifery care and home birth are regular options in low risk pregnancies. We aimed to examine women’s motivations for birthing outside the system in order to provide medical professionals with insight and recommendations regarding their interactions with women who have birth wishes that go against medical advice. Methods An exploratory qualitative research design with a constructivist approach and a grounded theory method were used. In-depth interviews were performed with 28 women on their motivations for going against medical advice in choosing a high risk childbirth setting. Open, axial and selective coding of the interview data was done in order to generate themes. A focus group was held for a member check of the findings. Results Four main themes were found: 1) Discrepancy in the definition of superior knowledge, 2) Need for autonomy and trust in the birth process, 3) Conflict during negotiation of the birth plan, and 4) Search for different care. One overarching theme emerged that covered all other themes: Fear. This theme refers both to the participants’ fear (of interventions and negative consequences of their choices) and to the providers’ fear (of a bad outcome). Where for some women it was a positive choice, for the majority of women in this study the choice for a home birth in a high risk pregnancy or an unassisted childbirth was a negative one. Negative choices were due to previous or current negative experiences with maternity care and/or conflict surrounding the birth plan. Conclusions The main goal of working with women whose birthing choices do not align with medical advice should not be to coerce them into the framework of protocols and guidelines but to prevent negative choices. Recommendations for maternity caregivers can be summarized ...