The size and morphology of the active phase (metal or metal oxide) are critical for the performance of heterogeneous catalysts. Conventional approaches for catalyst synthesis involve the modification of pore size and structure, the use of ligands to anchor the metal during preparation or the use of nanostructured oxides with well-defined facets to provide suitable sites for metal nucleation and growth. However, these approaches may not yield durable catalysts for high temperature applications, such as the treatment of unburnt methane from natural gas fueled engines. Here we demonstrate an approach that relies on the trapping of metal single atoms on the support surface, in thermally stable form, to modify the nature of deposited metal/metal oxide clusters. By anchoring Pt ions on the catalyst support we can tailor the morphology of the deposited phase. In particular, two-dimensional (2-D) rafts of Pt/PtOx on the engineered catalyst support are formed by this approach, as opposed to three-dimensional (3-D) metal oxide nanoparticles on conventional supports. Adopting this approach for the synthesis of bimetallic catalysts via addition of Pd to the atom-trapped catalyst support (Pt@CeO2) we found that the resulting Pd/Pt@CeO2 catalyst provides improved thermal stability and water tolerance during methane oxidation. We attribute the improved performance to the 2-D morphology of the Pd/PdO phase present on the atom-trapped catalyst support. The results show that modifying the support by trapping single atoms could provide an important addition to the toolkit of catalyst designers to engineer catalyst supports for controlling the nucleation and growth of metal and metal oxide clusters in heterogeneous catalysts.