In the present study, Bi2Te3 thin films and bulk nanocomposites, with varying concentration of Graphene (G), Silicon(Si) and Carbon (C) have been synthesized. The G, Si and C phases have been introduced inside grains and at the grain boundaries to enhance the thermoelectric performance of the Bi2Te3 nanocomposites. The effect of concentration of G, Si and C secondary phase segregated along Bi2Te3 crystallite boundaries on electrical and thermal properties of Bi2Te3 nanocomposite has been investigated. The effect of different nanoinclusions on growth and structural properties has been discussed in detail. The effect of concentration on the thermal conductivity of Bi2Te3 nanocomposites at nanoscale level was investigated using scanning thermal microscopic studies. The value of thermal conductivity for the composite samples was determined using modified Parker’s method. A commercial SThM system was modified by incorporating a microcontroller driven microhotplate. The radial thermal conductivity of Bi2Te3 and Bi2Te3:Si at around 70 °C is calculated to be 1.15 W/mK and 0.57 W/m K, respectively. Incorporation of optimized concentration of Si resulted in change in electronic properties due to modification in crystallite orientation, and phonon transport due to the presence of a secondary conducting phase along Bi2Te3 crystallites. This resulted in higher electron transport and increased phonon scattering leading to enhanced ZT ~ 1.4 for Bi2Te3:Si and ZT ~ 0.92 for Bi2Te3:G composite samples. Enhanced value of ZT for Bi2Te3:G sample in comparison to Bi2Te3:C sample highlights the advantage of using 2D materials at interfaces for increased phonon scattering without affecting the electron transfer. The present study presents a novel route for simultaneous control of phonon as well as electron transport to decouple the unfavorably coupled thermoelectric parameters. Further this study is important for establishing the role of secondary phase along crystallite boundaries leading to enhanced thermoelectric performance.