Introduction: Endometriosis is a chronic disease affecting 5–10% of women in the reproductive age. Despite surgical and medical treatment, many women struggle with pain, infertility, sexual dysfunction, depression, distress and reduced workability, affecting their overall quality of life. The usual follow-up procedures may not support the women’s self-management of this condition. Therefore, person-centred empowerment-based approaches are needed. Aim: To assess if the implementation of the Guided Self-Determination method targeted women with complex endometriosis appeared feasible and supported self-management. Methods: Guided Self-Determination was offered to 10 out-patients with complex endometriosis. Each of the women had five conversations based on prefilled disease-specific reflection sheets. A qualitative evaluation was conducted in 2016–2017 covering semi-structured, telephone interviews and focus group interviews, which were analysed using thematic analysis. Additionally, we assessed if the women changed the self-reported questionnaires, Endometriosis Health Profile 30 and the Patient Activation Measure from before and after the conversations. Results: We identified four themes: feeling alone with the disease; establishing a meaningful relationship with healthcare professionals in a traditional hospital setting; person-specific knowledge facilitated new behaviours and; accepting a chronic condition – the beginning of a process. All dimensions of the Endometriosis Health Profile 30 and the Patient Activation Measure appeared to improve at two weeks and so did almost all the dimensions of Endometriosis Health Profile 30 after 1 year. Conclusions: The implementation of the Guided Self-Determination method appeared feasible and the women developed self-management skills in relation to endometriosis and its symptoms. This was achieved by increasing insight into their needs and behaviours and gaining new knowledge about the disease itself. The before-and-after assessment suggested benefit of the intervention, but this should be further tested in a randomised trial.