Unmanned aerial vehicle (UAV)‐acquired multispectral images commonly suffer from radiometric inaccuracies due to changing illumination produced by intermittent cloud cover. This study addressed cloud shadow effects by integrating direct irradiance measurements from a downwelling light sensor into reflectance calculations. Two reflectance calibration methods were proposed as follows: (1) use of a single calibration reference panel for all images (Method 1) and (2) employment of a minimum distance classifier to assign color‐graded in‐field reflectance calibration targets to individual images based on their proximity in irradiance levels (Method 2). Images were acquired from 30 and 75 m flight altitudes with fixed‐exposure and auto‐exposure settings. Conventional photogrammetric calibration of UAV multispectral images inadequately addressed cloud shadows, resulting in orthomosaics with poor to moderate spatial uniformity (R2 = 0.70–0.92) and high mean absolute percentage error (MAPE = 13.52%–49.18%). The proposed calibration methods improved radiometric accuracy, yielding average R2 = 0.99 and 0.98 at 30 and 75 m images, respectively. Method 1 showed superior performance on the red‐edge and near infrared bands, and Method 2 worked best in the blue, green, and red bands. Post‐processing empirical line calibration of orthomosaics from Methods 1 and 2 reduced MAPE in reflectance estimation by at least 50% compared to conventional calibration. The clear sky reference histograms had lower Jensen–Shannon distance, higher Pearson's correlation, and improved intersection ratios with the histograms from the proposed methods, implying high similarity. Vegetation indices calculated with the proposed methods closely matched those from the reference orthomosaic, exhibiting significantly lower MAPE than conventionally calculated vegetation indices.