(1) Background: “Kidney Disease: Improving Global Outcomes” (KDIGO) provides guidelines for identifying the stages of acute kidney injury (AKI) and chronic kidney disease (CKD). A data-driven rule-based engine was developed to determine KDIGO staging compared to KD-related keywords in discharge letters. (2) Methods: To assess potential differences in outcomes, we compare the patient subgroups with exact KDIGO staging to imprecise or missing staging for all-cause mortality, in-hospital mortality, selection bias and costs by applying Kaplan–Meier analysis and the Cox proportional hazards regression model. We analysed 63,105 in-patient cases from 2016 to 2023 at a tertiary hospital with AKI, CKD and acute-on-chronic KD. (3) Results: Imprecise and missing CKD staging were associated with an 85% higher risk of all-cause and in-hospital mortality (CI: 1.7 to 2.0 and 1.66 to 2.03, respectively) compared to exact staging for any given disease status; imprecise or missing AKI staging increased in-hospital mortality risk by 56% and 57% (CI: 1.43 to 1.70 and 1.37 to 1.81, respectively) in patients with AKI. (4) Conclusions: Exact staging is associated with better outcomes in KD management. Our study provides valuable insight into potential quality and outcome improvements and lower costs, considering elderly patients, women and patients with acute-on-chronic KD as the most vulnerable.