This cross-sectional study aimed to estimate the prevalence of obesity and its association with diabetes and hypertension among beneficiaries in the National Guard Health Affairs system of Saudi Arabia. We included individuals aged 17 years and older, and patients were classified as diabetic or hypertensive if they had any visit during the 4 years where the primary diagnosis was one of those conditions or they were taking diabetes or hypertension medications. The association between obesity (body mass index ≥30) and diabetes and hypertension were evaluated using a multiple logistic regression model, adjusting for age, gender, nationality, and region. A total of 616,092 individuals were included. The majority were Saudi nationals (93.1%). Approximately 68% of the population were either obese (38.9%) or overweight (29.30%). Obesity was more prevalent among Saudi nationals (39.8% vs. 26.7%, p < 0.01) and females (45.3% vs. 31.2%, p < 0.01). Obesity was independently associated with diabetes mellitus (OR = 2.24, p < 0.01) and hypertension (OR = 2.15, p < 0.01). The prevalence of obesity in the study population was alarming and more pronounced among women. Our findings call for efforts to intensify preventive measures to reduce obesity and associated conditions. Using electronic records to examine the impact of interventions to reduce obesity and chronic conditions may help monitor and improve population health.