Complex nanoparticles, which contain multiple elements, crystal structures, and architectures, are useful for elucidating principles of fundamental thermodynamics and can be applied in fields spanning catalysis to plasmonics. However, the combinations of elements that have been explored thus far in these systems are limited by a lack of combinatorial methods for preparing multiplexed nanoparticle systems. In this presentation, we will discuss how correlative electron microscopy can be used to study the structures and dynamics of complex nanoparticles generated in scanning probe-deposited polymer nanoreactors. Metal, oxide, and hybrid metal-oxide nanoparticles of a variety of compositions and structures can be rapidly generated on electron-transparent substrates with exquisite site-specificity. These particles can then be easily relocated multiple times, enabling repeated, correlated characterization at the individual nanoparticle level. Moreover, polymer nanoreactors provide a viable platform for studying coarsening and solvent-particle interactions at the nanoscale and can be analyzed using in situ electron microscopy. This work demonstrates how polymer nanoreactors, when combined with advanced electron microscopy techniques, can be used as a versatile methodology for understanding the structure–function relationships as well as the formation mechanisms of complex nanoparticles, especially during their synthesis and processing.