Three organotin carboxylate species stabilized by the same ligands, but varying in size and structure, were studied to elucidate the effects of the structure on reactivity in the context of direct-write electron beam patterning. The chemical reactions that occur between the organotin reagents and the electron beam, the patterned film products, and the ligand decomposition and desorption byproducts were compared across all species. We found that both the metal−oxo content and the ligand coordination mode of each organotin reagent affected the reaction efficiency during electron beam patterning. In each case, an insoluble metal−oxo product formed after irradiation, but the composition, structure, and surface morphology of the products were nearly indistinguishable from the initial films. Examining the byproducts of the irradiation chemistry using electron-stimulated desorption confirmed that many of the organic ligands remained in the film during the reaction, likely crosslinking the clusters together to form a metal−oxo polymer product. Finally, we discuss the implications of the chemical transformations that occur during patterning for the use of these organotin reagents as both photoresists for lithography and direct-write functional nanomaterials.