Type 2 diabetes mellitus (T2DM) represents a growing public health concern in Indigenous populations, where early risk identification remains limited. This study aimed to analyze the association between estimated T2DM risk and cardiorespiratory endurance in a Zenú Indigenous community in northern Colombia. A cross-sectional study was conducted among adults aged 18–70 years belonging to the Momil Urban Minor Indigenous Cabildo (Córdoba, Colombia). T2DM risk was assessed using the Finnish Diabetes Risk Score (FINDRISC), and cardiorespiratory endurance was evaluated through the Ruffier index. Associations were examined using a multivariable ordinal logistic regression model, and discriminative performance was evaluated using receiver operating characteristic (ROC) curve analysis. A total of 95 participants were included, most of whom were classified as low risk according to FINDRISC, while cardiorespiratory endurance assessed by the Ruffier index was predominantly classified as moderate to good. Age was significantly associated with higher risk categories in the adjusted model, whereas cardiorespiratory endurance was not significantly associated with estimated T2DM risk. The model demonstrated excellent discriminative capacity (AUC = 0.912; 95% CI: 0.850–0.973). In this population, age and family history were key determinants of estimated T2DM risk. Findings regarding cardiorespiratory endurance should be interpreted cautiously given sample size limitations.