Alcohol use disorder (AUD) represents a major public health challenge, with current pharmacological and psychotherapeutic treatments showing limited efficacy. Recent clinical evidence suggests that MDMA-assisted psychotherapy may be effective for AUD, although concerns remain regarding its safety and potential for recreational use. This study investigated the effects of MDMA administration on alcohol intake in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats, a well-established model of excessive drinking, and examined its impact on the dynorphin/κ-opioid receptor (DYN/KOR) and nociceptin/orphanin FQ-NOP (N/OFQ-NOP) gene expression. These peptidergic systems are intrinsically dysregulated in msP rats, across key brain regions involved in addiction and emotional processing, including the amygdala (AMY), ventral tegmental area (VTA), and nucleus accumbens (NAc). Repeated intraperitoneal MDMA administrations (8 mg/kg for 5 consecutive days) rapidly reduced ethanol consumption without affecting anxiety-like behavior. Molecular analyses revealed that repeated ethanol exposure upregulated dynorphin expression and altered pN/OFQ-NOP mRNA levels in the AMY and VTA. MDMA treatment reduced dynorphin and Oprk1 expression and modulated nociceptin system gene expression in the AMY and VTA of alcohol-preferring rats. These adaptations were region-specific and were not observed in the NAc. Guided by these results we microinjected MDMA (0.3, 1.0, and 10 μg/0.5 μL/side) into the central amygdala (CeA). In an additional experiment MDMA (10 μg/0.5 μL/side) was administered into the VTA. Results showed a significant reduction in ethanol intake following intra-CeA administration 24 h post-injection. No effects were detected after intra-VTA treatment in the tested experimental condition. Overall, these findings indicate the ability of MDMA to decrease ethanol intake in msP rats and to induce gene expression alterations of dynorphinergic and nociceptinergic systems within specific mesolimbic brain regions.