Scientific challenges that underlie efficient energy storage, chemical conversions and separations, and quantum computing may be addressed using unconventional mass spectrometry techniques that provide unprecedented molecular-level insight. Novel materials not obtainable through conventional synthesis methods may be prepared using a versatile deposition approach known as ion soft landing. A wide range of polyatomic ions, clusters, and nanoparticles with precise composition and charge may be delivered to supports with predetermined coverage and kinetic energy, thereby circumventing the heterogeneity, contamination, and aggregation that often confound characterization and modeling of materials. In this presentation, I will illustrate several recent applications of ion soft landing in energy related research. Precisely controlling the size, shape, and elemental composition of alloy nanoparticles is central to developing catalysts that efficiently promote reactions. Magnetron sputtering combined with gas aggregation prepares bare ionic nanoparticles with unique composition and morphology that are size-selected and deposited onto electrodes. For energy storage, sub-nanometer metal oxides known as polyoxometalates are leading candidates for use in advanced molecular batteries and supercapacitors. Insights are obtained into how the redox properties of polyoxometalates evolve with metal substitution by leveraging the atom-by-atom selectivity of ion soft landing. The impact of substrate and intermolecular interactions on the vibrational properties of polyoxometalate-based molecular qubit arrays is investigated, as is the influence of the size and stoichiometry of ionic liquid clusters on the desolvation, reduction, and separation of metals ions at electrodes. Combined with state-of-the-art characterization techniques and high-level theoretical modeling, ion soft landing is providing transformative insights into the properties of materials in the size regime where each atom counts.