Metal promotion is broadly applied to enhance the performance of heterogeneous catalysts to fulfill industrial requirements. Still, generating and quantifying the effect of the promoter speciation that exclusively introduces desired properties and ensures proximity to or accommodation within the active site and durability upon reaction is very challenging. Recently, In₂O₃ was discovered as a highly selective and stable catalyst for green methanol production from CO₂. Activity boosting by promotion with palladium, an efficient H₂-splitter, was partially successful since palladium nanoparticles mediate the parasitic reverse water–gas shift reaction, reducing selectivity, and sinter or alloy with indium, limiting metal utilization and robustness. Here, we show that the precise palladium atoms architecture reached by controlled co-precipitation eliminates these limitations. Palladium atoms replacing indium atoms in the active In₃O₅ ensemble attract additional palladium atoms deposited onto the surface forming low-nuclearity clusters, which foster H₂ activation and remain unaltered, enabling record productivities for 500 h.