The chromatographic separation of plant pigments is one of the most popular and visually appealing experiments encountered by young scientists when they are introduced to the principles of analytical chemistry. As such, it has found widespread application in schools, public engagement activities, and undergraduate laboratories. However, most of the methods used in these contexts suffer from a range of limitations, including the difficulty of separating and isolating individual pigments when using paper-based or thin layer chromatography techniques or the need for specialized spaces in order to contain volatile, harmful solvents and dry silica powder. This new modular laboratory protocol has been developed following green chemistry principles and employs a series of inexpensive, bench-friendly methods. The protocol allows for the separation and quantitation of chlorophyll pigments in plant extracts through the use of prepacked, inexpensive reversed-phase chromatography columns and UV-vis spectrophotometry. A synthetic component is added to the more traditional separation experiments through the development of the bench-friendly synthesis of coloring agent E141, a chlorophyll-derived food dye. The protocol embeds analytical and mathematical components that encourage students to engage in problem solving activities and mathematical modeling early on in their studies.