Weather and climate models are increasingly used at kilometer-scale resolutions that develop a variety of secondary circulations, including horizontal roll vortices and cold pool gust fronts. Although these circulations are ubiquitous in convective boundary layers over land, their impacts on surface energy balance are largely unknown. Doppler lidar and surface observations were combined with DOE E3SM land model experiments, revealing increased surface winds (5 m/s) and heat fluxes (50 W/m²) in convergent branches of horizontal rolls. Larger wind-driven flux responses (up to 150 W/m²) were found along gust fronts. Surface energy balance shifts to accommodate wind-driven fluxes, reducing ground heat conduction and longwave cooling. Our findings from the US Southern Great Plains are broadly relevant to modeling convective boundary layers. In particular, widely-used subgrid wind gust parameterizations were found to be physically inconsistent with resolved secondary circulations and could worsen climate prediction biases at kilometer-scales.