Some paintings may have hidden depictions beneath the visible surface, which can provide valuable insights into the artist’s creative process and the genesis of the artwork. Studies have shown that these covered paintings can be revealed through image-based techniques and integrated data processing. This study analyzes an oil painting by Beceri from the mid-16th century depicting the Holy Family, owned by the Uffizi Galleries. During the analysis of the materials, we discovered evidence of pictorial layers beneath the visible scene. To uncover the hidden figuration, we applied a multimodal approach that included microprofilometry, reflectance imaging spectroscopy, macro X-ray fluorescence, and optical coherence tomography. We analyzed the brushstrokes of the hidden painting, visualized the underdrawing, located the painted areas beneath the outermost painting, and quantified the thicknesses of the pictorial layers. The pigments used for the underpainting were identified through cross-analysis of X-ray fluorescence and spectral correlation maps. The underlying pictorial subject, Leda and the Swan, appears to be inspired by a long-lost and replicated work by Michelangelo. This information places Beceri and his production in a more defined context.