Recombinant proteins are widely used for industrial purposes including manufacturing, pharmaceuticals, and beauty. Using microalgae as a biomanufacturing platform has piqued research interests due to their photosynthetic or heterotrophic capabilities and cellular machinery that has the ability to correctly fold and secrete many recombinant proteins. However, several obstacles remain, such as low heterologous protein expression and a lack of strong expression and secretion vectors specific to microalgae. Here we made progress toward a molecular biology tool to help overcome these challenges by easing the quantification of a secreted recombinant protein. This was achieved by fusing the recombinant protein to a self-cleaving viral peptide from the Foot and Mouth Disease Virus (FMDV), a secretion peptide, and a GFP fluorescent marker. By establishing the ratio of the GFP to the protein of interest, a quantification can be obtained of the secreted recombinant protein of interest by measuring GFP fluorescence. This work presents the basis for a polycistronic tool that offers a quick method of quantifying recombinant protein in the microalga Chlamydomonas reinhardtii for biotechnological and industrial purposes.