Bismuth-based materials show promise for aqueous energy storage systems due to their unique layered structures and high storage capacity. Some bismuth-based materials have been applied to storage Zn2+ or NH4+, indicating that one bismuth-based compound may be innovatively used in both zinc-ion and ammonium-ion batteries (ZIBs and AIBs). Herein, we successfully design a poly(3,4-ethylenedioxythiophene) (PEDOT) coated and embedded Bi2Te3 (Bi2Te3@PEDOT). Theoretical calculations and experimental researches demonstrate that the PEDOT coating and its intercalation into the interlayer enhance the structural stability of Bi2Te3 and significantly improve the storage capacities for Zn2+ and NH4+. The PEDOT intercalation results in an increased interlayer spacing and a charge redistribution in the interlayer, facilitating the charge transfer. Additionally, the insertion-type mechanism of Zn2+ and NH4+ in Bi2Te3@PEDOT is revealed through ex-situ tests. The optimized electrode (5 mg cm−2) exhibits high discharge capacities of 385 mA h g−1 in ZIBs and 235 mA h g−1 in AIBs at 0.2 A g−1 and a long-term cycle stability. Bi2Te3@PEDOT performs robustly even at a high mass loading of 10 mg cm−2. Bi2Te3@PEDOT//MnO2 (ZIBs) and Bi2Te3@PEDOT//ZnMn2O4 (AIBs) full cells offer high reversible capacities. This work provides a reference for designing bifunctional energy storage materials.