Background: The coexistence of Myasthenia Gravis (MG) and Rheumatoid Arthritis (RA) represents a rare but clinically challenging form of polyautoimmunity, raising interesting questions about shared immunopathogenic mechanisms and the safety of long-term immunomodulatory therapies. Methods: The article describes a case report of a 66-year-old female with a 12-year history of seropositive RA who subsequently developed seropositive MG during long-term exposure to hydroxychloroquine (HCQ) therapy. Following discontinuation of HCQ, methotrexate (MTX) therapy was initiated and stable control of both diseases was temporally obtained. Results: Three years later, the patient presented with upper gastrointestinal bleeding and severe microcytic anemia. Further evaluation revealed advanced liver fibrosis (F4) and severe gastropathy, consistent with Child–Pugh class A cirrhosis. Viral, alcoholic, and autoimmune causes of chronic liver disease were excluded. In the absence of alternative etiologies, this was considered possibly associated with MTX therapy, in the context of additional metabolic risk factors, including type 2 diabetes mellitus and increased body mass index. Conclusions: The complex interplay between polyautoimmunity and treatment-related toxicity is underscored in this article. Overlapping autoimmune diseases may arise on a shared immunological background, while therapeutic agents may contribute to disease expression or long-term complications. These findings highlight the need for individualized therapeutic strategies and vigilant monitoring, particularly in patients with coexisting metabolic risk factors.