Patients with an autoimmune disease could be at higher risk of a poor outcome when contracting COVID-19 infection due to aberrant immune responses and use of immunosuppressant therapies for chronic autoimmune treatment. Here, we conducted a retrospective study to identify the factors related to severity, hospitalization, and mortality among patients with autoimmune diseases. We found 165 cases of patients with pre-existing autoimmune diseases who had contracted COVID-19 between March 2020 and September 2022. Data on demographical characteristics; autoimmune diagnosis and treatment; COVID-19 vaccination status; and time, severity, and outcome of COVID-19 infection were collected. Most of the subjects were female (93.3%) and autoimmune diagnoses included systemic lupus erythematosus (54.5%), Sjogren’s syndrome (33.5%), antiphospholipid syndrome (23%), vasculitis (5.5%), autoimmune thyroid disease (3.6%), rheumatoid arthritis (3.03%), and inflammatory bowel disease (3.03%) among other autoimmune diseases. There were four COVID-19-related deaths in this study. Factors associated with moderate to severe COVID-19 infection in patients with autoimmune diseases included not being vaccinated against COVID-19, taking a steroid of ≥10 mg prednisone-equivalent per day, and having a cardiovascular disease. Taking a steroid of ≥10 mg prednisone-equivalent per day was also associated with hospitalization in the event of COVID-19 infection, while cardiovascular diseases also showed a significant correlation to mortality in patients with autoimmune diseases who had been hospitalized with COVID-19 infection.