Objective: It has been reported that monochorionic twin pregnancies conceived through assisted reproductive techniques (ART) display a higher risk of second-trimester miscarriage, cesarean delivery, and neonatal death than those conceived naturally. The aim of this study was to compare the perinatal outcomes of monochorionic diamniotic (MCDA) twin pregnancies conceived naturally and through ART in a tertiary hospital. Methods: This was a retrospective cohort study of all MCDA twin pregnancies that received obstetric care and delivered at La Fe University and Polytechnic Hospital between 2015 and 2021. MCDA pregnancies that were referred to the tertiary hospital for specialized management, follow-up, and delivery were also included. The study was approved by The Health Research Institute Hospital La Fe (IIS La Fe). Results: Among the 184 MCDA pregnancies, 149 (81%) had a natural conception, and 35 (19%) were conceived through ART. Patients with an MCDA pregnancy who conceived through ART had a significantly older maternal age (38.0 [35.5-42.5] vs. 32.0 [29.0-36.0], p < 0.001) and an elevated rate of nulliparity (80.0% vs. 50.3%, p = 0.001). Regarding pregnancy complications, MCDA pregnancies through ART were associated with a significantly higher incidence of gestational diabetes (22.9% vs. 2.7%, p < 0.001), hypertensive disorders during pregnancy (22.9% vs. 9.4%, p = 0.04), and other pregnancy complications such as threatened labor or preterm prelabor rupture of membranes (14.3% vs. 36.2%, p = 0.015), than naturally conceived MCDA pregnancies. No differences were found in the incidence of twin-to-twin transfusion syndrome (20% vs. 33.6%, p = 0.155). MCDA pregnancies through natural conception had a greater rate of vaginal delivery than MCDA through ART (16.8% vs. 2.9%, p = 0.032). When adjusted for confounding factors, MCDA pregnancies through ART were only more likely to develop gestational diabetes than those naturally conceived (aOR 7.86, 95% CI 1.55-39.87). No differences were found regarding neonatal outcomes between groups. Conclusions: Compared with naturally conceived MCDA twin pregnancies, those conceived through ART displayed a significantly higher risk of developing gestational diabetes. No differences regarding other pregnancy complications, mode of delivery, or neonatal outcomes were found between groups.