Bladder Cancer (BLCa) inter-patient heterogeneity is the primary cause of treatment failure, suggesting that patients could benefit from a more personalized treatment approach. Patient-derived organoids (PDOs) have been successfully used as a functional model for predicting drug response in different cancers. In our study, we established PDO cultures from different BLCa stages. PDOs preserve the histological and molecular heterogeneity of the parental tumors (PT), including their multiclonal genetic landscapes, and consistently share key genetic alterations detected in PTs, mirroring tumor evolution in longitudinal sampling. Our drug screening pipeline was implemented using PDOs, testing both standard-of-care and FDA-approved compounds for other tumors. Integrative analysis of drug response profiles with matched PDO genomic analysis was used to determine enrichment thresholds for candidate markers of therapy response and resistance. Finally, by assessing the clinical history of longitudinally sampled cases, the disease clonal evolution could be determined and matched with drug response.