(1) Background: We aimed to reveal the relationship between the choroid and the outer retina with optical coherence tomography (OCT) in patients with diabetes mellitus (DM) with mild or no diabetic retinopathy (DR) in order to find early biomarkers for progressing retinopathy. (2) Methods: We performed a prospective study including 61 eyes of patients with type 1 or type 2 DM and 36 eyes of healthy controls. All subjects were imaged with Spectralis OCT. The choroid was assesseed using enhanced depth imaging OCT (EDI-OCT). Binarization of subfoveal choroidal images was done with public domain software, ImageJ (version 1.53a; National Institutes of Health, Bethesda, Maryland, USA). (3) Results: Luminal area, stromal area and total choroidal area were significantly decreased in diabetic patients compared to control: 0.23 ± 0.07 vs. 0.28 ± 0.08, p = 0.012; 0.08 ± 0.03 vs. 0.10 ± 0.04, p = 0.026; 0.31 ± 0.09 vs. 0.38 ± 0.11, p = 0.008. The thickness of retinal pigment epithelium (RPE) correlated positively with the choroidal vascularity index (CVI). The correlations between outer nuclear layer (ONL), photoreceptors (PR) and foveal choroidal thickness (FChT) were moderately negative. (4) Conclusion: Thicker RPE and a thinner PR layer may be assigned the role of early biomarkers signaling the conversion time to progressing retinopathy.