The association between systemic sclerosis and other immune-mediated diseases such as primary sclerosing cholangitis and hyperthyroidism should be suspected in case the patient presents with similar symptoms. A 43-year-old woman presented to the hospital with progressive jaundice, dark urine, dyspnoea, fatigue, generalized arthralgia, weight loss, and amenorrhoea. In addition, she was diagnosed with systemic sclerosis seven years ago. The patient was diagnosed recently with primary sclerosing cholangitis and hyperthyroidism through laboratory tests and investigations such as magnetic resonance cholangiopancreatography, ultrasound, and computed tomography scan. After appropriate treatment and follow-up, the patient recovered well. Immune-mediated diseases can occur simultaneously or consequently due to the common immunological dysfunction that causes these conditions.