This dataset contains images, color features, and postharvest quality analysis data from indoor growing microgreens. Image bank contains raw images of 9 species of microgreens grown indoors under different light intensities, obtained under different colors of light source, as well as the regions of interest extracted from each image. Dataset includes the color attributes extracted from the images, physicochemical and pigment analysis data. All python scripts for all steps of pre-processing, processing, modeling and validation of non-destructive machine learning methods for estimating pigment content are available.