To further our understanding of Leonardo da Vinci’s painting practices, a new scientific research study was conducted on Ginevra de' Benci, c. 1474/1478. More information about the preparatory underdrawing, undermodeling, and palette was obtained. The new analysis included multispectral infrared reflectography at high spatial resolution (50 μm per pixel) in three spectral bands between 1000 and 2500 nm. These high-resolution infrared images were registered to the digital X-ray radiograph and color image of the painting. This allowed careful comparison of specific compositional features among the color, infrared and X-ray images which helped to deduce the paint layering sequence. A false-color infrared reflectogram helped to better visualize the undermodeling present in the face of Ginevra, as well as the pounced dots used to initially position the sitter. Finally, the pigments used were determined from non-invasive chemical point analysis using reflectance and X-ray fluorescence spectroscopies, which were found to be consistent with Leonardo’s known palette. The combination of multispectral infrared reflectography, the ability to register the images from multiple imaging methods, and the knowledge obtained about the pigments provides a more comprehensive understanding about the underdrawing and painting process of Ginevra de' Benci.