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Introduction Osteoporosis and fragility fracture are more frequently found in systemic lupus erythematosus (SLE) patients than in normal population. This study aims to determine the risk factors in SLE patients in a tertiary hospital in Indonesia.Methods This is a cross-sectional study involving patients with SLE according to the 1997 American College of Rheumatology (ACR) criteria or 2019 ACR/EULAR classification criteria, from the rheumatology clinic in Dr. Soetomo General Academic Hospital. Subject characteristics data were extracted from medical records, and dual X-ray absorptiometry was performed on all the subjects to measure the lumbar spine and femoral neck bone mineral density (BMD), Z-score and T-score.Result Data from 152 subjects were collected. 27% of subjects had osteoporosis and the mean age was 34.63±10.42-year old. Lower body mass index (BMI) (B 0.074; p 0.004), higher disease activity (B 0.054; p 0.04), corticosteroid use (B −0.018; p 0.036) and older age (B −0.027; p 0.003) were significantly associated with lower T-score. In particular, higher age was associated with lower femoral neck BMD, while menopause was correlated to lower lumbar spine and total hip BMD. The use of azathioprine (AZA) (OR 0.225; CI 0.051 to 0.990; p 0.048) and hydroxychloroquine (HCQ) (OR 0.293; CI 0.115 to 0.746; p 0.01) was associated with a lower incidence of osteoporosis.Conclusion The prevalence of osteoporosis in the SLE population was 26.97%. Ageing, menopause, lower BMI, higher current disease activity and higher cumulative dose of corticosteroids were associated with low BMD in our study. Risk factor for osteoporosis in our study was lower BMI, menopause and the use of high dose steroids. The use of AZA and HCQ appeared to be protective for osteoporosis.