An integrated circuit containing CMOS transistors and an embedded thermoelectric device may be formed by forming field oxide in isolation trenches to isolate the CMOS transistors and thermoelectric elements of the embedded thermoelectric device. N-type dopants are implanted into the substrate to provide at least 1×1018 cm−3 n-type dopants in n-type thermoelectric elements and the substrate under the field oxide between the n-type thermoelectric elements. P-type dopants are implanted into the substrate to provide at least 1×1018 cm−3 p-type dopants in p-type thermoelectric elements and the substrate under the field oxide between the p-type thermoelectric elements. The n-type dopants and p-type dopants may be implanted before the field oxide are formed, after the isolation trenches for the field oxide are formed and before dielectric material is formed in the isolation trenches, and/or after the field oxide is formed.