The lack of energy balance closure in Eddy-Covariance (EC) measurements is a well-known, still unresolved challenge in micrometeorology, with energy balance closure (EBC) rates typically ranging between 60% and 80%. While numerous hypotheses have been proposed to explain this imbalance, the relative contributions of neglected energy storage terms, data quality and flux processing options remain insufficiently disentangled. Using standardized ICOS and NEON datasets, we show that a significant portion of the observed energy imbalance can be attributed to overlooked or inconsistently handled energy components and turbulent flux quality control. Using data drawn from 84 sites, we show that comprehensive energy accounting—including soil heat flux, storage terms (soil, air, biomass), photosynthetic energy demand, and strict quality filtering of turbulent fluxes—improved EBC by 16% on average, with site-specific gains up to 40%. However, we also identify a persistent residual imbalance that is unlikely to be resolved through methodological refinements or additional measurements alone, pointing to fundamental physical processes that are not accounted for in the standard measurement and processing. We argue that this unresolved imbalance should be explicitly acknowledged and bounded, rather than implicitly absorbed into correction schemes, and we outline practical guidance for diagnosing and interpreting EBC in standardized flux networks. This perspective evaluates methodological advances and residual uncertainties, providing an actionable framework for the appropriate use of EC energy fluxes in carbon, water, and climate research.