Underground thermal energy storage (UTES) use has showed a sharp rise in numbers in the last decades, with aquifer thermal energy storage (ATES) and borehole thermal energy storage (BTES) most widely used. In many urban areas with contaminated aquifers, there exists a desire for sustainable heating and cooling with UTES and a need for remediation. We investigated the potential synergy between UTES and bioremediation with batch experiments to simulate the effects of changing temperature and liquid exchange that occur in ATES systems, and of only temperature change occurring in BTES systems on cis-DCE reductive dechlorination. Compared to the natural situation (NS) at a constant temperature of 10 °C, both UTES systems with 25/5 °C for warm and cold well performed significantly better in cis-DCE removal. The overall removal efficiency under mimicked ATES and BTES conditions were respectively 13 and 8.6 times higher than in NS. Inoculation with Dehalococcoides revealed that their initial presence is a determining factor for the dechlorination process. Temperature was the dominating factor when Dehalococcoides abundance was sufficient. Stimulated biodegradation was shown to be most effective in the mimicked ATES warm well, due to the combined effect of suitable temperature, sustaining biomass growth and regular cis-DCE supply.