Many plasma membrane receptors and ligands form nanoscale clusters on the plasma membrane surface. However, methods for directly and precisely manipulating nanoscale protein localization are limited, making understanding the effects of this clustering difficult. DNA origami allows precise control over nanoscale protein localization with high fidelity and adaptability. Here, we describe how we have used this technique to study how nanoscale protein clustering affects phagocytosis. We provide protocols for conjugating DNA origami structures to supported lipid bilayer-coated beads to assay phagocytosis and planar glass coverslips for TIRF microscopy. The core aspects of this protocol can be translated to study other immune signaling pathways and should enable the implementation of previously inaccessible investigations.