Background/Objectives: This study aims to investigate the long-term effect of inactive systemic lupus erythematosus (SLE) on the retinal microcirculation measured via optical coherence tomography angiography (OCT-A). Methods: Twenty-four eyes of 24 patients with inactive SLE under hydroxychloroquine (HCQ) therapy were included. The OCT-A data (mainly vessel density (VD) and foveal avascular zone (FAZ) data of the superficial and of the deep capillary plexus (SCP, DCP) and the choriocapillaris (CC)) were analyzed and compared between the baseline examination (t0) and 2 years later (t1). Results: At t1, VD in the whole en face SCP and in the CC was notably reduced compared to t0 (SCP: p = 0.001, CC: p = 0.013). VD in the DCP, CRT and FAZ area showed no difference at t1 compared to t0 (DCP: p = 0.128, FAZ: p = 0.332, CRT fovea: p = 0.296). Correlation analysis between the increase in cumulative doses of HCQ between t0 and t1 and the VD of the whole en face SCP did not show any correlation (Spearman r = 0.062 (95% CI −0.367; 0.477). Conclusions: SLE patients demonstrated a decrease in the retinal VD of the SCP and CC over a 2-year period. There was no correlation with the change in cumulative doses of HCQ. These results suggest an ongoing effect of the disease on the retinal and choriocapillary microcirculation.