(1) Background: This paper illustrates an innovative methodological approach chosen to study and map the colors of the Medieval wall painting of Santa Maria Antiqua in the Roman forum, one of the pilot sites of the EHEM project (Enhancement of Heritage Experiences: The Middle Ages. Digital Layered Models of Architecture and Mural Paintings over Time); (2) Methods: We chose to use two methods for gathering information about colors and mapping, specifically colorimetry by spot measurements and hypercolorimetric multispectral imaging (HMI) to map those same colors sampled through colorimetry; (3) Results: Chromatic data of all colors in the wall paintings were obtained in the CIELAB color space. In those same points, chromatic similarity maps were performed by the innovative HMI system, a multispectral imaging technique able to obtain also color data information by means of the advanced calibration software named SpectraPick®: this allowed to have a complete knowledge of the color characteristics and distribution; (4) Conclusion: The color measurements and mapping was an important result to improve the reading of Medieval wall paintings, fragmentary and stratigraphically complex, giving a new light in the knowledge of the colors and allowing to better understand the original appearance of the iconographic patterns, reconstructed with colors as faithfully as possible similar to the originals.