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Livestock agriculture accounts for ∼15% of global anthropogenic greenhouse gas (GHG) emissions. Recently, natural climate solutions (NCS) have been identified to mitigate farm‐scale GHG emissions. Nevertheless, their impacts are difficult to quantify due to farm spatial heterogeneity and effort required to measure changes in carbon stocks. Remote sensing (RS) models are difficult to parameterize for heterogeneous agricultural landscapes. Eddy covariance (EC) in combination with novel techniques that quantitatively match source area variations could help update such vegetation‐specific parameters while accounting for pronounced heterogeneity. We evaluate a plant physiological parameter, the maximum quantum yield (MQY), which is commonly used to calculate gross and net primary productivity in RS applications. RS models often rely on spatially invariable MQY, which leads to inconsistencies between RS and EC models. We evaluate if EC data improve RS models by updating crop specific MQYs to quantify agricultural GHG mitigation potentials. We assessed how farm harvest compared to annual sums of (a) RS without improvements, (b) EC results, and (c) EC‐RS models. We then estimated emissions to calculate the annual GHG balance, including mitigation through plant carbon uptake. Our results indicate that EC‐RS models significantly improved the prediction of crop yields. The EC model captures diurnal variations in carbon dynamics in contrast to RS models based on input limitations. A net zero GHG balance indicated that perennial vegetation mitigated over 60% of emissions while comprising 40% of the landscape. We conclude that the combination of RS and EC can improve the quantification of NCS in agroecosystems.