Objective: To assess whether the care model (comprehensive vs regular) has any impact on the clinical outcomes of systemic lupus erythematosus patients. Methods: Between August 2019 and January 2020, we evaluated SLE patients being cared for at two Peruvian hospitals to define the impact of care model on disease activity state and health-related quality of life (HRQoL). Disease activity was ascertained with the SLEDAI-2K and the Physician Global Assessment (PGA) which allows to define Lupus Low Disease Activity State (LLDAS) and Remission. HRQoL was measured with the LupusQoL. The association between care model and disease activity (Remission and LLDAS) state was examined using a binary logistic regression model. The association with HRQoL was examined with a linear regression model. All multivariable analyses were adjusted for possible confounders. Results: 266 SLE patients were included, 227 from the comprehensive care model and 39 from the regular care model. The regular care model was associated with a lower probability of achieving remission (OR 0.381; CI: 95% 0.163–0.887) and LLDAS (OR 0.363; CI: 95% 0.157–0.835). Regular care was associated with a better HRQoL in two domains (pain and emotional health). We found no association between the care model and the other HRQoL domains. Conclusion: A comprehensive care model was associated with the probability of achieving remission and LLDAS but had no apparent impact on the patients’ HRQoL.