Purpose: This study aims to assess the effect of bariatric surgery on retinal microvascular calibre, peripheral microvascular function, peripheral pressure waveforms, and the general cardiovascular disease (CVD) risk in obese individuals after undergoing Roux-en-Y gastric bypass (RYGB) surgery. Methods: A total of 29 obese participants were included in the study. All of the measurements were conducted at two time points: before and one year following the bariatric surgery procedure. General anthropometric data, as well as blood markers for glucose, cholesterol, and triglycerides were assessed in all individuals. In all participants, the Framingham risk score (FRS), and retinal vessel calibre measurements, using a Zeiss fundus camera and VesselMap software (ImedosSystems, Jena, Germany), were performed. Systemic arterial stiffness was measured by pulse wave analysis (PWA), and peripheral microvascular reactivity by way of digital thermal monitoring (DTM) in all participants. Results: As expected, various general anthropometric parameters, including body mass index (BMI), waist circumference and neck circumference, were significantly decreased post-surgery comparing to baseline in all individuals (all p < 0.001). In addition, their general CVD risk, as measured using FRS, was significantly improved (p < 0.001). At the retinal vascular level, central retinal artery equivalent (CRAE) as well as, central retinal vein equivalent (CRVE) had increased after surgery comparing to the baseline values (p = 0.003 and p = 0.007, respectively). In addition, both systemic arterial stiffness and peripheral microvascular reactivity had improved in all participants (p < 0.001 and p = 0.008 respectively). Conclusions: Our findings suggest that bariatric surgery has a positive effect on the overall vascular health, as well as on the general CVD risk of the obese patients undergoing this procedure.