Over the past decades, significant advancements have been made in various medical fields; however, ovarian cancer (OC) remains inadequately addressed, predominantly relying on relatively toxic cytostatic treatments. In this study, we applied newly developed poly(β-amino) esters (PBAEs) for siRNA delivery. As recent literature has shown, the introduction of a hydrophobic, unsaturated fatty acid together with polycationic spermines as the PBAE side chains are leading to a favourable transfection efficiency, and the resulting materials form a unique class of micelleplexes, termed micelle-embedded polyplexes (mPolyplexes). Here, such mPolyplexes were modified post-particle formation with the approved monoclonal antibody Trastuzumab for HER2 targeting, as supported by a receptor binding analysis through fluorescence shift assay. Physicochemical analysis revealed suitable hydrodynamic diameters of modified mPolyplexes, as determined by dynamic light scattering. Improved cellular uptake when targeted with Trastuzumab was optimized by applying Design of Experiment (DoE). We demonstrated superior gene silencing efficiency of EGFR as well as PLK1, both involved in OC progression, with knockdown values exceeding 82% and 70%, respectively. These findings were corroborated by a relevant cell migration assay. The macroscopic impact after PLK1 silencing on epithelial-mesenchymal transition (EMT) was visualized using confocal microscopy. This work addresses critical questions in the field of ovarian cancer therapy and confirms the suitability of siRNA encapsulating PBAE nanocarriers as promising non-viral vectors.