Background: To test clinically relevant factors associated with quantitative artifact-free deep capillary plexus (DCP) metrics in patients with diabetes mellitus (DM). Methods: 563 eligible eyes (221 with no diabetic retinopathy [DR], 135 with mild DR, 130 with moderate DR, and 77 with severe DR) from 334 subjects underwent optical coherence tomography-angiography (OCT-A) with a swept-source OCT (Triton DRI-OCT, Topcon, Inc., Tokyo, Japan). Strict criteria were applied to exclude from analysis those DCP images with artifacts and of poor quality, including projection artifacts, motion artifacts, blurriness, signal loss, B-scan segmentation error, or low-quality score. A customized MATLAB program was then used to quantify DCP morphology from the artifact-free DCP images by calculating three metrics: foveal avascular zone (FAZ), vessel density (VD), and fractal dimension (FD). Results: 166 (29.5%) eyes were excluded after quality control, leaving in the analysis 397 eyes (170 with no DR, 101 with mild DR, 90 with moderate DR, 36 with severe DR) from 250 subjects. In the multiple regression models, larger FAZ area was associated with more severe DR (β = 0.687; p = 0.037), shorter axial length (AL) (β = − 0.171; p = 0.003), thinner subfoveal choroid thickness (β = − 0.122; p = 0.031), and lower body mass index (BMI) (β = − 0.090; p = 0.047). Lower VD was associated with more severe DR (β = − 0.842; p = 0.001), shorter AL (β = 0.107; p = 0.039), and poorer visual acuity (VA) (β = − 0.133; p = 0.021). Lower FD was associated with more severe DR (β = − 0.891; p < 0.001) and with older age (β = − 0.142; p = 0.004). Conclusions: Quantitative artifact-free DCP metrics are associated with VA, DR severity, AL, subfoveal choroidal thickness, age, and BMI in diabetic patients. The effects of ocular and systemic factors should be considered for meaningful interpretations of DCP changes in DM patients.