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Abstract Van der Waals (vdW) heterostructures that pair materials with diverse properties enable various quantum phenomena. However, the direct growth of vdW heterostructures is challenging. Modification of the surface layer of quantum materials to introduce new properties is an alternative process akin to solid state reaction. Here, vapor deposited transition metals (TMs), Cr and Mn, are reacted with Bi₂Se₃with the goal to transform the surface layer to XBi₂Se₄(X = Cr, Mn). Experiments and ab initio MD simulations demonstrate that the TMs have a high selenium affinity driving Se diffusion toward the TM. For monolayer Cr, the surface Bi₂Se₃is reduced to Bi₂‐layer and a stable (pseudo) 2D Cr_1+δSe₂layer is formed. In contrast, monolayer Mn can transform upon mild annealing into MnBi₂Se₄. This phase only forms for a precise amount of initial Mn deposition. Sub‐monolayer amounts dissolve into the bulk, and multilayers form stable MnSe adlayers. This study highlights the delicate energy balance between adlayers and desired surface modified layers that governs the interface reactions and that the formation of stable adlayers can prevent the reaction with the substrate. The success of obtaining MnBi₂Se₄points toward an approach for the engineering of other multicomponent vdW materials by surface reactions.