Clean combustion, i.e., the reduction of NOx and soot emissions, and carbon neutrality, achieved in part by biofuel synthesis, are major milestones in the transition to a sustainable future. To overcome empiric and time-consuming process optimization steps, we need detailed reaction mechanistic and chemical insights on these processes. Be it in combustion or in catalysis, highly reactive intermediates, such as radicals, carbenes, and ketenes drive chemical reactions. Knowing the fate of these species helps develop strategies to optimize chemical energy conversion processes. This calls for advanced mass spectrometric tools, which enable the detection of transient species. In this review, we report on the application of state-of-the-art photoelectron photoion coincidence (PEPICO) spectroscopy with vacuum ultraviolet (VUV) synchrotron radiation as advanced diagnostic tools in catalysis and combustion research. We discuss reaction mechanisms in biomass conversion to sustainable fuels, where we report on the pyrolysis of wood samples probed using VUV photoionization mass spectrometry (PIMS) and obtain deep mechanistic insights in the (non)catalytic pyrolysis of lignin model compounds with PEPICO detection. PEPICO is also shown to contribute to the mechanistic understanding of catalysis by unveiling catalytic alkane valorization mechanisms. We discuss how PEPICO detection advances combustion diagnostics, thanks to the application of photoelectron spectroscopy and velocity map imaging. We report on mechanistic aspects of ignition, such as fuel radical formation and oxidation to peroxy species, and discuss reaction pathways of pollutant formation. In addition, we zoom into the elementary reactions of combustion and discuss isomer-selective kinetics experiments on radical oxidation. Newly revealed reaction pathways to polycyclic aromatic hydrocarbon (PAH) formation are also detailed. Finally, we describe current instrumental developments to improve PEPICO detection and report on innovative sources, reactors, and reaction sampling approaches to be combined with this technique.