In this study, we aim to evaluate the factors that may contribute to the development of chronic kidney disease following COVID-19 infection among hospitalized patients in two private hospitals in Jakarta, Indonesia. This is a retrospective cohort study between March 2020 and September 2021. Patient selection was conducted with a convenience sampling. All patients (n = 378) meeting the inclusion criteria during the study period were enrolled. Various sociodemographic, laboratory test, and diagnostic parameters were measured before the determination of their correlation with the outcome of COVID-19 infection. In this study, all pre-vaccinated patients with COVID-19 had no history of chronic kidney disease (CKD) prior to hospital admission. From this number, approximately 75.7% of the patients developed CKD following COVID-19 diagnosis. Overall, significant correlations were established between the clinical outcome and the CKD status (p = 0.001). Interestingly, there was a significant correlation between serum creatinine level, glomerular filtration rate (GFR), and CKD (p < 0.0001). Oxygen saturation (p = 0.03), admission to the intensive care unit (ICU) (p < 0.0001), and sepsis (p = 0.005) were factors that were significantly correlated with CKD status. Additionally, the type of antibiotic agent used was significantly correlated with CKD (p = 0.011). While 82.1% of patients with CKD survived, the survival rate worsened if the patients had complications from hyperuricemia (p = 0.010). The patients who received levofloxacin and ceftriaxone had the highest (100%) survival rate after approximately 50 days of treatment. The patients who received the antiviral agent combination isoprinosine + oseltamivir + ivermectin fared better (100%) as compared to those who received isoprinosine + favipiravir (8%). Factors, such as hyperuricemia and the antibiotic agent used, contributed to CKD following COVID-19 hospitalization. Interestingly, the patients who received levofloxacin + ceftriaxone and the patients without sepsis fared the best. Overall, patients who develop CKD following COVID-19 hospitalization have a low survival rate.