Single point eddy covariance measurements of the Earth’s surface energy budget frequently identify an imbalance between available energy and turbulent heat fluxes. While this imbalance lacks a definitive explanation, it is nevertheless a persistent finding from single-site measurements; one with implications for atmospheric and ecosystem models. This has led to a push for intensive field campaigns with temporally and spatially distributed sensors to help identify the causes of energy balance non-closure. Here we present results from the Chequamegon Heterogeneous Ecosystem Energy-balance Study Enabled by a High-density Extensive Array of Detectors 2019 (CHEESEHEAD19)—an observational experiment designed to investigate how the Earth’s surface energy budget responds to scales of surface spatial heterogeneity over a forest ecosystem in northern Wisconsin. The campaign was conducted from June–October 2019, measuring eddy covariance (EC) surface energy fluxes using an array of 20 towers and a low-flying aircraft. Across the domain, energy balance residuals were found to be highest during the afternoon, coinciding with the period of surface heterogeneity-driven mesoscale motions. The magnitude of the residual varied across different sites in relation to the vegetation characteristics of each site. Both vegetation height and height variability showed positive relationships with the residual magnitude. During the seasonal transition from latent heat-dominated summer to sensible heat-dominated fall the magnitude of the energy balance residual steadily decreased, but the energy balance ratio remained constant at 0.8. This was due to the different components of the energy balance equation shifting proportionally, suggesting a common cause of non-closure across the two seasons. Additionally, we tested the effectiveness of measuring energy balance using spatial EC. Spatial EC, whereby the covariance is calculated based on deviations from spatial means, has been proposed as a potential way to reduce energy balance residuals by incorporating contributions from mesoscale motions better than single-site, temporal EC. Here we tested several variations of spatial EC with the CHEESEHEAD19 dataset but found little to no improvement to energy balance closure, which we attribute in part to the challenging measurement requirements of spatial EC.