Obesity is strongly associated with cardiovascular diseases (CVD) and type 2 diabetes (T2D). This study aimed to use obesity measures, body mass index (BMI) and waist circumference (WC) to predict the CVD and T2D risk and to determine the best predictor of these diseases among Jordanian adults. A cross-sectional study was conducted at the governmental and military hospitals across Jordan. The study participants were healthy or previously diagnosed with CVD or T2D. The continuous variables were compared using ANOVA, and the categorical variables were compared using the X2 test. The multivariate logistic regression was used to predict CVD and T2D risk through their association with BMI and WC. The final sample consisted of 6000 Jordanian adults with a mean age of 41.5 ± 14.7 years, 73.6% females. The BMI (OR = 1.7, CI: 1.30–2.30, p < 0.001) was associated with a higher risk of T2D compared to WC (OR = 1.3, CI: 1.04–1.52, p = 0.016). However, our results showed that BMI was not associated with CVD risk, while the WC was significantly and positively associated with CVD risk (OR = 1.9, CI: 1.47–2.47, p < 0.001). In conclusion, an elevated BMI predicts a higher risk of T2D, while WC is more efficient in predicting CVD risk. Our results can be used to construct a population-specific intervention to reduce the risk of CVD and T2D among adults in Jordan and other countries with similar backgrounds.