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.