Adequate surgical management of malignant endometriosis remains a clinical challenge in gynecology. Age, sonography variables, and tumor biomarkers have been reported as candidates in the clinical decision. This study aims were to analyze the factors of women’s age, body mass index, ultrasound features, and tumor biomarkers to predict endometriosis-associated ovarian cancer in a large series of endometriomas and to study the surgical treatment performed in this cohort. In this retrospective study, we reviewed the medical records of patients with ultrasound diagnosis of ovarian cyst classified as endometrioma (benign as well as with risk of malignancy), surgically treated in the endometriosis unit of Hospital Universitario La Paz (Madrid, Spain) between January 2019 and July 2021. According to the final histology examination, the women were clustered as non-endometriosis-associated ovarian cancer (OE, benign endometriomas, n = 59) and endometriosis-associated ovarian cancer (EAOC) (n = 17). Demographic, clinical, and surgical data were collected from these women. International Ovarian Tumor Analysis (IOTA) criteria were assessed for the ultrasound examination. The age of the women in the EAOC group was 50.0 [43.0; 63.0] years, which was significantly higher than OE (39.0 [34.0; 46.0] years; p-value < 0.001). In addition, the body mass index for the OE group (24.9 ± 5.3 kg/m2) was significantly higher than for the EAOC group (23.3 ± 4.6 kg/m2; p-value < 0.001). However, the tumor biomarker levels (CA 125, CA 19.9 and He4) were not significantly different among the groups. We performed 51.4% cystectomies and 48.6% adnexectomies, with an association between the adnexectomy and EAOC group (p-value < 0.001). In addition, a significant association was found between ultrasound features suspicious for malignancy and the EAOC group. Conclusively, women’s age and ultrasound features, such as papillary projections, septa, and positive echo-Doppler, were the main factors to consider when evaluating the malignancy risk associated with endometriosis.