Understanding and controlling nanomaterial structure, chemistry, and defects represents a synthetic and characterization challenge. Metal-organic frameworks (MOFs) have recently been explored as unconventional precursors from which to prepare nanomaterials. Here we use in situ X-ray pair distribution function analysis to probe the mechanism through which MOFs transform into nanomaterials during pyrolysis. By comparing a series of bimetallic MOFs with trimeric node different compositions (Fe3, Fe2Co, and Fe2Ni) linked by carboxylate ligands in a PCN-250 lattice, we demonstrate that the resulting nanoparticle structure, chemistry, and defect concentration depend on the node chemistry of the original MOF. These results suggest that the preorganized structure and chemistry of the MOF offer new potential control over the nanomaterial synthesis under mild reaction conditions. In the case of Fe2Ni-PCN-250, selective extraction of one Ni ion from each node without collapsing the framework (i.e., node-ligand connectivity) leaves a metal-deficient MOF state that may provide a new route to post-synthetically tune the chemistry the MOF and subsequent nanomaterials.