Long-term ecosystem–atmosphere flux measurements are crucial for understanding land–atmosphere interactions, ecosystem functioning, and climate variability. In West Africa’s Sudanian savanna, such data are limited despite rapid land use change and high climate sensitivity. We address this by providing a harmonized, multi-site eddy covariance dataset of carbon, water, and energy fluxes from six savanna ecosystems in Burkina Faso and Ghana.</p> <p>The dataset provides half-hourly and daily turbulent CO<sub>2</sub>, latent and sensible heat fluxes, net radiation, meteorological variables, and, where available, soil moisture and soil temperature. Measurements span the period 2013–2025 across contrasting land-use types ranging from forest savanna to cropland and degraded grassland. All data were processed with a uniform EddyPro-based workflow and further post-processed to ensure physical plausibility, temporal consistency, and harmonized variable definitions. Quality flags accompany all turbulent fluxes for user-defined filtering.</p> <p>Archived in the PANGAEA repository and openly available (DOI: <a href="https://doi.org/10.1594/PANGAEA.994143" target="_blank" rel="noopener">https://doi.org/10.1594/PANGAEA.994143</a>), the dataset’s temporal continuity, explicit quality information, and multi-year coverage support diverse applications, including land surface and Earth system model evaluation, land–atmosphere coupling studies, satellite and machine-learning product validation, and analyses of seasonal to interannual variability and hydroclimatic extremes. These long-term, quality-controlled flux observations from a climate-sensitive, underrepresented region provide a key resource for advancing process understanding and model development in West African savannas.