This study evaluates the antimicrobial, antioxidant, and anticancer effects of Brazilian red propolis extract (BRPE) and its nanoencapsulated form (NCBRPE) to address bacteria and conditions associated with the ovarian cancer microenvironment. The NCBRPE showed an average size of 178.3 ± 3.3 nm, a polydispersity index (PdI) of 0.06, and an encapsulation efficiency exceeding 97% for the main bioactive compounds of propolis. Antimicrobial assays revealed that BRPE exhibited minimum inhibitory concentrations (MICs) ranging from 4 to 256 mg/L against seven bacterial strains, while NCBRPE demonstrated sustained efficacy, with a biofilm inhibitory concentration (BIC) of 128 mg/L against Burkholderia cepacia. In clonogenic assays, NCBRPE reduced long-term cancer cell proliferation, achieving a 10-fold decrease in colony formation compared to untreated controls, significantly outperforming BRPE. Flow cytometry indicated that NCBRPE induced apoptosis in 29% ± 0.4 of ovarian cancer cells (OVCAR-3). Additionally, the DPPH assay confirmed the antioxidant activity of NCBRPE, demonstrating that it retained most of the extract’s original antioxidant capacity. This was further supported by oxidative burst assays, which showed a significant reduction in reactive oxygen species (ROS) production in neutrophils. These findings position NCBRPE as a multi-functional therapeutic candidate for managing infections, oxidative stress, and tumor progression in the ovarian cancer microenvironment.