To evaluate different quantitative non-invasive retinal biomarkers of microvascular impairment and neurodegeneration in patients affected by mild and moderate non proliferative diabetic retinopathy (NPDR) with or without macular microaneurysms (MAs). A cross-sectional case-control study. Ninety-seven eyes with NPDR, 49 with no central MAs and 48 with central MAs, underwent color fundus photography and optical coherence tomography (OCT)/OCT-angiography (OCT-A). Thickness of central macula, retinal nerve fiber layer (NFL), ganglion cell layer (GCL+) and NFL + GCL + was evaluated on OCT. FAZ metrics (ImageJ), perfusion and vessel density (PD/VD), and fractal dimension (FD) (MATLAB) were evaluated on 3 × 3 OCT-A slabs of both superficial and deep capillary plexuses (SCP/DCP). All evaluations were performed on the full image and after subdivision in 4 quadrants. In the MA group, 77 MAs were detected (45.5% in the DCP). The MA group showed: increased FAZ area and perimeter in the SCP (p < 0.01) and DCP (p = 0.02), and reduced circularity index in the SCP (p = 0.03); reduced VD in the SCP (p < 0.01) and reduced PD, VD (p < 0.01) and FD (p = 0.02) in the DCP; decreased VD and FD in the SCP (p = 0.02 and p = 0.05), and in VD and FD in the DCP in the inferior quadrant (p = 0.04 and p = 0.03); a decrease in VD in the SCP in the nasal quadrant (p = 0.05). No differences have been detected in OCT parameters. Our results suggest that the presence of central MAs in patients with NPDR may correlate with more pronounced macular microvascular impairment, particularly during the mild and moderate stages of the disease.