Objectives: This study aims to determine whether the MetS predicts damage accrual in SLE patients. Methods: This longitudinal study was conducted in a cohort of consecutive SLE patients seen since 2012 at one single Peruvian institution. Patients had a baseline visit and then follow-up visits every 6 months. Patients with ≥ 2 visits were included. Evaluations included interview, medical records review, physical examination, and laboratory tests. Damage accrual was ascertained with the SLICC/ACR damage index (SDI) and disease activity with the SLEDAI-2K. Univariable and multivariable Cox-regression survival models were carried out to determine the risk of developing new damage. The multivariable model was adjusted for age at diagnosis; disease duration; socioeconomic status; SLEDAI; baseline SDI; the Charlson Comorbidity Index; daily dose; and time of exposure of prednisone (PDN), antimalarials, and immunosuppressive drugs. Results: Two hundred and forty-nine patients were evaluated; 232 of them were women (93.2%). Their mean (SD) age at diagnosis was 35.8 (13.1) years; nearly all patients were Mestizo. Disease duration was 7.4 (6.6) years. The SLEDAI-2K was 5.2 (4.3) and the SDI, 0.9 (1.3). One hundred and eight patients (43.4%) had MetS at baseline. During follow-up, 116 (46.6%) patients accrued at least one new point in the SDI damage index. In multivariable analyses, the presence of MetS was a predictor of the development of new damage (HR: 1.54 (1.05–2.26); p < 0.029). Conclusions: The presence of MetS predicts the development of new damage in SLE patients, despite other well-known risk factors for such occurrence.