BackgroundForced migration significantly endangers health. Women face numerous health risks, including sexual violence, lack of contraception, sexually transmitted disease, and adverse perinatal outcomes. Therefore, sexual and reproductive healthcare is a significant aspect of women asylum seekers’ health.Even when healthcare costs of asylum seekers are covered by the government, there may be strong barriers to healthcare access and specific needs may be addressed inadequately. The study’s objectives were a) to assess the accommodation and healthcare services provided to women asylum seekers in standard and specialised health care, b) to assess the organisation of healthcare provision and how it addresses the sexual and reproductive healthcare needs of women asylum seekers.MethodsThe study utilised a multi-method approach, comprising a less-dominant quantitative component and dominant qualitative component. The quantitative component assessed accommodation conditions for women in eight asylum centres using a survey. The qualitative component assessed healthcare provision on-site, using semi-structured interviews with health and social care professionals (n = 9). Asylum centres were selected to cover a wide range of characteristics. Interview analysis was guided by thematic analysis.ResultsThe accommodation in the asylum centres provided gender-separate rooms and sanitary infrastructure. Two models of healthcare were identified, which differed in the services they provided and in their organisation: 1) a standard healthcare model characterised by a lack of coordination between healthcare providers, unavailability of essential services such as interpreters, and fragmented healthcare, and 2) a specialised healthcare model specifically tailored to the needs of asylum-seekers. Its organisation is characterised by a network of closely collaborating health professionals. It provided essential services not present in the standard model. We recommend the specialised healthcare model as a guideline for best practise.ConclusionsThe standard, non-specialised healthcare model used in some regions in Switzerland does not fully meet the healthcare needs of women asylum seekers. Specialised healthcare services used in other regions, which include translation services as well as gender and culturally sensitive care, are better suited to address these needs. More widespread use of this model would contribute significantly toward protecting the sexual and reproductive integrity and health of women asylum seekers.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3502-2) contains supplementary material, which is available to authorized users.