Background While most countries that allow abortion on women’s request also grant physicians a right to conscientious objection (CO), this has proven to constitute a potential barrier to abortion access. Conscientious objection is regarded as an understudied phenomenon the effects of which have not yet been examined in Germany. Based on expert interviews, this study aims to exemplarily reconstruct the processes of abortion in a mid-sized city in Germany, and to identify potential effects of conscientious objection. Methods Five semi-structured interviews (...) with experts from all instances involved have been conducted in April 2020. The experts gave an insight into the medical care structures with regard to abortion procedures, the application and manifestations of conscientious objection in medical practice, and its impact on the care of pregnant women. A content analysis of the transcribed interviews was performed. Results Both the procedural processes and the effects of conscientious objection are reported to differ significantly between early abortions performed before the 12th week of pregnancy and late abortions performed at the second and third trimester. Conscientious objection shows structural consequences as it is experienced to further reduce the number of possible providers, especially for early abortions. On the individual level of the doctor-patient relationship, the experts confirmed the neutrality and patient-orientation of the vast majority of doctors. Still, it is especially late abortions that seem to be vulnerable to barriers imposed by conscientious objection in individual medical encounters. Conclusion Our findings indicate that conscientious objection possibly imposes barriers to both early and late abortion provision and especially in the last procedural steps, which from an ethical point of view is especially problematic. To oblige hospitals to partake in abortion provision in Germany has the potential to prevent negative impacts of conscientious objection on women’s rights on an individual as well as on a structural level. (shrink)