Materials that can host Majorana zero modes gained a lot of attention in recent years due to the possibility to engineer topologically protected quantum computing platforms. Promising candidates are heterostructures of topological insulators and superconductors. Here we present density-functional-theory-based calculations for Pd-doped Bi₂Te₃ and Pd(Bi,Te)x (x=1,2) in order to shed light on the superconducting properties in the self-formed superconducting phase when Pd is deposited on top of the topological insulator Bi₂Te₃. This dataset accompanies a joint experiment/theory publication and publishes the related density functional theory calculations for: - relaxed geometries for Pd intercalation in the Bi₂Te₃ vdW gap - electronic structure of PdTe and PdTe₂ compared to alloy phases of Pd(Bi,Te) and Pd(Bi,Te)₂, collectively referred to as "xPBT" - calculations for the superconducting state of xPBT phases within the Kohn-Sham Bogoliubov-de Gennes method