The need for alternative energy sources has led to extensive research on optimizing the conversion efficiency of thermoelectric (TE) materials. TE efficiency is governed by figure-of-merit (ZT) and it has been an enormously challenging task to increase ZT > 1 despite decades of research due to the interdependence of material properties. Most doped inorganic semiconductors have a high electrical conductivity and moderate Seebeck coefficient, but ZT is still limited by their high lattice thermal conductivity. One approach to address this problem is to decrease thermal conductivity by means of alloying and nanostructuring, another is to consider materials with an inherently low thermal conductivity on account of their disordered structure such as polymers and optimize their power factor through doping. In the first part of this dissertation, thermal transport in nanostructures of silicon-based Group-IV alloys is studied by employing the phonon Boltzmann transport formalism with full phonon dispersion and a partially diffuse momentum-dependent specularity model for boundary roughness scattering. Results show thermal conductivity in Si-Ge nanostructures to be well below their bulk counterparts and tunable by extrinsic boundary effects such as sample size in thin films, period thickness in superlattices, length/diameter in nanowires, and grain size in nanocomposites. Additionally, boundary/interface properties, such as roughness, orientation, and composition, significantly affect transport and offer additional degrees of freedom to control thermal conductivity. The latter part of the dissertation examines the effects of disorder on TE properties of semiconducting polymers based on the Gaussian disorder model for site energies, while employing Pauli’s master equation approach to model hopping between localized sites. Disorder leads to inherently different transport, and results show that minimizing energetic disorder and correlation while increasing positional disorder results in a higher TE power factor. While doping increases charge carrier density, long-range Coulomb interactions between dopant molecules and localized carriers broadens the electronic density-of-states. The width and shape of density-of-states, dictated by dopant distribution, governs the trade-off relationship between electrical conductivity and Seebeck coefficient. It is shown that dopant-induced energetic disorder can be overcome by increasing dopant size and dielectric permittivity, improving charge screening and transport, resulting in a higher power factor.