Endometriosis affects a great proportion of women during their reproductive years and may impair female fertility in several ways. Ovarian endometrioma (OE) is the most frequent phenotype and growing evidence suggest an endometrioma-mediated damage to the ovary, ovarian reserve and oocyte quality. Traditionally, surgery has been the first-line treatment in cases of OE. Great advances in assisted reproduction and fertility preservation techniques opened new possibilities towards a more conservative approach. Herein we discuss multiple mechanisms responsible for the deterioration of the reproductive capacity in cases of OE as well as the pros and cons of different treatment options. The management of endometrioma-related subfertility remains controversial and it will depend on patient's intentions and priorities. In the "internet era" patients tend to be hyper-informed and more participative, but they are often misguided and misinformed. Thus, doctors should be able to convert these individuals into well-informed patients in order to facilitate the process of shared decision making, which is extremely relevant in the context of OEs.