In 2021, the National Kidney and Transplant Institute released the second edition of its glomerulonephritis handbook to standardize the treatment of IgA nephropathy, a prevalent primary glomerular disease in Asia. This study aimed to evaluate patient response and outcomes to the protocol-directed management implemented from 2021 to 2023. This study is a retrospective observational analysis. Binary logistic regression was performed to identify factors associated with therapy response and overall patient. Associations with risk classifications and IgAN variants were assessed, rejecting null hypotheses at 0.05 α-level significance. Adherence to protocol at baseline showed significant better therapy responses with 60.23% achieved complete remission as while those who deviated from the protocol had 2.82% complete remission. Adherence to the protocol was also associated with markedly better outcomes. Regarding overall patient outcomes, the majority of patients (57.02%, 95% CI: 50.52–63.30) were alive at the end of the study period. Patients classified as low risk had the most favorable therapy responses observed over 24 months. However, it was noted that progression to end-stage renal disease was significantly more frequent in the intermediate-risk group (47.37%) at 24 months likewise reflecting a lower survival rate of the group (39.47%) at 12 months indicating disease progression despite therapy. The findings align by demonstrating improved long-term therapy response and outcomes through early and sustained risk stratification, along with adherence to protocol-directed management,. particularly for those classified as low risk or without variant forms. Conversely, high-risk classifications and aggressive variants such as AKI and RPGN are associated with significantly poorer responses and survival rates, necessitating close monitoring and more aggressive interventions. Efforts to reduce loss to follow-up, optimize patient retention, and personalize therapy are essential to enhancing long-term outcomes.