The interdependency among thermal conductivity, electrical conductivity, and the Seebeck coefficient acts as a challenge to enhancing thermoelectric (TE) performance. However, thanks to nanotechnology, it is possible to break this interdependency by employing the phonon glass electron crystal (PGEC) approach. The present work aims to decrease the lattice thermal conductivity by inducing nanoflower-like structures in a conducting polymer matrix. Herein, we report the thermoelectric properties of graphene oxide and titanium dioxide (GO–TiO2) quantum dots (QDs) in poly(3,4-ethylene dioxythiophene):polystyrene sulfonate (PEDOT:PSS). The effect of QDs on the thermoelectric performance of the PEDOT:PSS polymeric matrix has been investigated experimentally and then analyzed using several theoretical models. The obtained nanocomposite showed an enhancement in Seebeck coefficient and electrical conductivity while decreasing lattice thermal conductivity. Furthermore, the filler successfully broke the interdependent relationship of thermoelectric parameters due to the existence of energy-filtering phenomena and interfacial thermal resistance.