Purpose Clinically, repeat renal biopsies (RRBs) have been performed in lupus nephritis to identify changes in class, plan treatment and assist in prognostication. We set out to compare the histopathological features and outcomes of disease flare and protocol biopsy patients. Methods A retrospective descriptive study was conducted on repeat biopsies performed between January 1984 and December 2015 in lupus nephritis patients. Disease flares and protocol biopsies were compared. Results Of 614 systemic lupus erythematosus (SLE) renal biopsies, 127 (20.7%) RRBs were identified. Disease flare patients accounted for 96 (75.6%) and protocol biopsies for 31 (24.4%) of RRBs. Seventy (72.9%) disease flare patients retained their original class on repeat biopsy. When categorised as proliferative and non-proliferative histology, 83 (87.4%) of the disease flare biopsy patients remained histologically unchanged. Treatment remained unchanged in 57 (60.0%) patients following RRBs for disease flares. Response to immunosuppression in disease flare patients was poorer. Non-response was associated with increased chronicity index (OR = 1.33; 95% CI 1.01-1.76; p = 0.045). Thirty-three (36.3%) disease flare patients developed end-stage kidney disease (ESKD) in one year as compared to one (3.6%) protocol biopsy patient ( p = 0.003). ESKD in disease flare patients was associated with non-response to treatment (OR = 24.6; 95% CI 2.7-219.3; p = 0.004) on multivariate analysis. One-year mortality was 30.0% in the disease flare patients and 3.5% in protocol biopsy patients ( p = 0.018). Conclusion Repeat biopsies in disease flare patients infrequently led to histological class changes, failed to lead to change of treatment in the majority of patients, and were associated with poorer outcomes.