Background: Endometriosis and adenomyosis are two closely related, estrogen-dependent, benign gynecological diseases. The available evidence on their common pathogenesis and association is limited and often does not address the heterogeneity of both entities. The aim of our study is to investigate the association between different types and localizations of adenomyosis and endometriosis phenotypes, using magnetic resonance imaging (MRI) and laparoscopic findings. Methods: We performed a retrospective observational study involving premenopausal women over 18 years old who underwent laparoscopic surgery for endometriosis and were pre-operatively diagnosed with adenomyosis through MRI examination at the Cantonal Hospital of Schaffhausen, Switzerland between 2011 and 2022. Results: Of 130 patients with adenomyosis, 23 (17.7%) women had adenomyosis only in the anterior wall (group 1), 38 (29.2%) only in the posterior wall (group 2), and 69 (53.1%) in both the anterior and posterior wall (group 3). Women in group 1 experienced significantly more dysuria compared to the two other groups (p = 0.018), while the prevalence of other pain symptoms (dysmenorrhea, dyspareunia, dyschesia) was comparable between the groups. Women in group 3 had significantly thicker anterior and posterior myometrium compared to groups 1 and 2 (p < 0.001). Co-existence of deep rectal endometriosis was more frequent in women from group 3 compared to groups 1 and 2 (p = 0.039) and in women with adenomyosis in the outer (extrinsic) compared to adenomyosis in the inner myometrium (intrinsic) (p < 0.001). Conclusions: This study provides evidence of an association between the localization of adenomyosis and the distribution of concomitant endometriosis. Specifically, adenomyosis localized in both the anterior and posterior wall appears to be more proliferative compared to adenomyosis found only in the anterior or posterior wall. This is indicated by its association with higher uterine volume, thicker posterior junctional zone, and greater myometrial thickness and with a higher co-existence with deep rectal endometriosis. These findings support an association between the development of specific subtypes of both entities, which represents a valuable resource for the identification of future targets for the treatment and clinical management of adenomyosis and endometriosis.