Objective: This cross-sectional study evaluated the association of plasma cytochrome c (CytoC) and hypoxia-inducible factor (HIF)-1α, as mitochondrial dysfunction and cellular hypoxia biomarkers, with disease risk factors and prognosis in Type 2 diabetic patients in Saudi Arabia. Methods: A total of 252 patients (94 males and 158 females) were eligible and were matched by socioeconomic status, age and body mass index (BMI) with 106 healthy participants (71 males and 35 females). They were subgrouped according to BMI, disease duration and treatment. Lipid and glycaemic control indices were colorimetrically measured to calculate insulin resistance (IR) and atherogenic index of plasma (AIP). Haemoglobin A1c, C-reactive protein (CRP), CytoC and HIF-1α were measured using specific immunoassays. Results: Among the patients, 50% (38.64% of males and 52.53% of females), 40.48% (43.18% of males and 40.51% of females), 4.365% (6.82% of males and 3.80% of females), 2.381% (4.55% of males and 1.90% of females), and ~0.8% (males) suffered from peripheral neuropathy, ophthalmopathy, kidney disease, myocardial infarction and ketoacidosis, respectively. The majority of complicated cases had greater age, BMI, disease duration, plasma insulin and AIP, and were on insulin. The two investigated groups were non-significantly different considering CytoC, but highly significantly different considering lipid profile (as reflected on AIP) and glycaemic control parameters (as reflected on IR, plasma CRP and HIF-1α), with significant correlations among all of them in a group-specific pattern. Conclusion: Patients suffered a high rate of complications that correlated with age, BMI, disease duration, AIP, plasma insulin and insulin treatment due to poor disease control. Reduced HIF-1α and non-significant increased CytoC levels correlated negatively with bad prognostic indicators of the disease pointing to a pathogenetic implication.