Gross primary productivity (GPP) has been reported to increase with the fraction of diffuse solar radiation, for a given total irradiance. The correlation between GPP and diffuse radiation suggests effects of diffuse radiation on canopy light‐use efficiency, but potentially confounding effects of vegetation phenology have not been fully explored. We applied several approaches to control for phenology, using 8 years of eddy‐covariance measurements of winter wheat in the U.S. Southern Great Plains. The apparent enhancement of daily GPP due to diffuse radiation was reduced from 260% to 75%, after subsampling over the peak growing season or by subtracting a 15 day moving average of GPP, suggesting a role of phenology. The diffuse radiation effect was further reduced to 22% after normalizing GPP by a spectral reflectance index to account for phenological variations in leaf area index LAI and canopy photosynthetic capacity. Canopy photosynthetic capacity covaries with diffuse fraction at a given solar irradiance at this site because both factors are dependent on day of year or solar zenith angle. Using a two‐leaf Sun‐shaded canopy radiative transfer model, we confirmed that the effects of phenological variations in photosynthetic capacity can appear qualitatively similar to the effects of diffuse radiation on GPP and therefore can be difficult to distinguish using observations. The importance of controlling for phenology when inferring diffuse radiation effects on GPP raises new challenges and opportunities for using radiation measurements to improve carbon cycle models.