Due to their inherent physical properties, thin-film Si/SiGe heterostructures have specific thermal management applications in advanced integrated circuits and this in turn is essential not only to prevent a high local temperature and overheat inside the circuit, but also generate electricity through the Seebeck effect. Here, we were able to enhance the Seebeck effect in the germanium composite quantum dots (CQDs) embedded in silicon by increasing the number of thin silicon layers inside the dot (multi-fold CQD material). The Seebeck effect in the CQD structures and multi-layer boron atomic layer-doped SiGe epitaxial films was studied experimentally at temperatures in the range from 50 to 300 K and detailed calculations for the Seebeck coefficient employing different scattering mechanisms were made. Our results show that the Seebeck coefficient is enhanced up to ≈40% in a 3-fold CQD material with respect to 2-fold Ge/Si CQDs. This enhancement was precisely modeled by taking into account the scattering of phonons by inner boundaries and the carrier filtering by the CQD inclusions. Our model is also able to reproduce the observed temperature dependence of the Seebeck coefficient in the B atomic layer-doped SiGe fairly well. We expect that the phonon scattering techniques developed here could significantly improve the thermoelectric performance of Ge/Si materials through further optimization of the layer stacks inside the quantum dot and of the dopant concentrations.