This study was designed to explore the impact of a managed care system on the morbidity and mortality rates in a systemic lupus erythematosus (SLE) cohort in Puerto Rico. The clinical manifestations and outcome measures of public SLE patients, before and after implementation of the managed care system, were compared with those of SLE patients treated in a private fee-for-service system. Of the cohort of 171 patients, 103 (60%) were treated in the public system and 68 (40%) in the private sector. Except for higher prevalence of hematuria, renal insufficiency, and serositis in the public group, both groups had a similar prevalence of clinical manifestations, Systemic Lupus Erythematosus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage score, and mortality rate before introduction of the managed care system. Six years after implementation of the managed care system, medically indigent patients were more likely to have photosensitivity (90% vs. 75%), malar rash (85% vs. 65%), hematuria (43% vs. 24%), nephrotic syndrome (17% vs. 6%), and end-stage renal disease (8% vs. 0%). They also had a higher mortality rate (10% vs. 2%) and SLICC/ACR damage index score (1.5 vs. 0.8). In summary, SLE patients treated in the public system of Puerto Rico demonstrated higher morbidity and mortality after being treated in a managed care system compared with patients managed in a private fee-for-service system. Different from the fee-for-service system, the managed care system seeks medical care cost reductions that could affect the management and outcome of SLE patients. These differences could also be related to the higher disease severity before implementation of the managed care system and lower socioeconomic status of the public group. Nevertheless, the public managed care system in Puerto Rico requires continuous evaluation to ensure SLE patients better access to specialty and subspecialty healthcare and optimal pharmacologic treatments.