Purpose This study aims to comparatively evaluate the morphological changes of the cornea after phacoemulsification (PHACO) and femtosecond laser-assisted cataract surgery (FLACS) without intercurrences in patients with type 2 diabetes mellitus. Methods A total of 95 diabetic patients with moderate cataracts (N2 + and N3+), 47 undergoing PHACO and 48 undergoing FLACS, were selected randomly for the study. Surgeries were performed by a single surgeon between July 2021 and December 2021. Cumulative dissipated energy (CDE) and total balanced saline solution (BSS) data were obtained at the end of each surgery. Changes in corneal endothelial cell density (ECD) and central corneal thickness (CCT) at three months postoperatively were investigated. Results After three months, evidence is lacking between groups in the CCT measures; the difference was neither statistically nor clinically relevant. However, for ECD, a significant and clinically significant difference was found; if all patients were treated with laser, the mean ECD would be 423.55 greater (RSE: 86.09; p-value < 0.001; 95% CI: 254.81–592.29) than the ECD potential means of 1656.423 among the conventional group (RSE: 74.90; p-value < 0.001; 95% CI: 1509.62–1803.23). Conclusions Diabetic patients under treatment with moderate cataracts may predispose themselves to a more significant loss of endothelial cells after conventional phacoemulsification than femtosecond laser-assisted cataract surgery. Trial registration It was registered at The Brazilian Registry of Clinical Trials (ReBEC) with the code RBR-6d8whb5 (UTN code: U1111-1277-6020) on 17/05/2022.