Three-dimensional organoid culture offers great promise for precision medicine in cancer. In this study, we describe label-free imaging procedures including Fluorescence Lifetime Imaging Microscopy (FLIM) and Raman microscopy allowing in situ cellular analysis and metabolic monitoring of drug treatment efficacy. Primary tumor as well as urine specimens were utilized to assemble a biobank of bladder cancer organoids. Organoids, recapitulating histopathological and molecular diversity were cultured in Matrigel and treated for several days with various concentrations of pharmaceutical agents relevant for treatment of bladder cancer (i.e. cisplatin, venetoclax). The effects of different drugs on cell metabolism were assessed by the local fluorophore environment of NADH and FAD determined by multiexponential fitting of lifetime decays. Direct cellular response upon drug treatment was monitored by Raman microspectroscopy. Via multivariate data analysis, Raman spectra of treated and untreated bladder cancer organoids were compared to reveal the effects of drugs on subcellular structures such as nuclei and mitochondria based on shifts and intensity changes of specific molecular vibrations. Drug-specific modes of action were reflected and discriminated in the metabolic profiles and molecular composition of the tumor models. Together, FLIM and Raman imaging are technologies allowing non-invasive and molecular-sensitive monitoring of tumor-drug interactions, providing the potential to determine and optimize patient-specific treatment efficacy.