Reporter-gene activation studies are essential for dissecting gene regulatory mechanisms, yet traditional whole-plant assays are often low-throughput and difficult to quantify. This chapter presents a streamlined method for analyzing reporter-gene activity using transiently transformed Arabidopsis thaliana mesophyll protoplasts. We describe the use of the pBeaconRFP vector for positive-fluorescent selection, enabling the isolation of successfully transformed cells via flow cytometry and fluorescence-activated cell sorting. Additionally, we introduce the pEvTV Gateway-compatible vector for flexible reporter-gene construct delivery and an automated pipeline for reproducible flow-cytometric data analysis. These methods facilitate rapid, robust, and scalable quantification of transcriptional responses, exemplified by the activation of the DR5 auxin-responsive reporter by gain-of-function Auxin Response Factor expression. The protocols are adaptable to other tissues and species, offering a versatile platform for high-throughput functional genomics.