Prostate cancer is a common cancer in men in older age groups. The WHO forecasts an increase in the incidence of prostate cancer in the coming years. Patients may not respond to treatment, and may not tolerate the side effects of chemotherapy. Compounds of natural origin have long been used in the prevention and treatment of cancer. Flavonoids obtained from natural products, e.g., propolis, are compounds with proven antibacterial and antiviral efficacy which modulate the immune response and may be useful as adjuvants in chemotherapy. The main aim of the present study was to evaluate the cytotoxic and pro-apoptotic properties of selected flavonoids on prostate cancer cells of the LNCaP line. The compounds used in this study were CAPE, curcumin (CUR), and quercetin (QUE). Mitochondrial and lysosome metabolism was assessed by the XTT-NR-SRB triple assay as well as by the fluorescent staining techniques. Staining for reactive oxygen species was performed as well. The experiment showed that each of the tested compounds has a cytotoxic effect on the LNCaP cell line. Different types of cell death were induced by the tested compounds. Apoptosis was induced by quercetin, while autophagy-specific changes were observed after using CAPE. Compounds obtained from other bee products have antiproliferative and cytotoxic activity against LNCaP prostate cancer cells.