Over the past ten years, research into students' emotions in educational environments has increased. Although researchers have called for more studies that rely on objective measures of emotional experience, limitations on utilizing multi-modal data sources exist. Studies of emotion and emotional regulation in classrooms traditionally rely on survey instruments, experience-sampling, artifacts, interviews, or observational procedures. These methods, while valuable, are mainly dependent on participant or observer subjectivity and is limited in its authentic measurement of students' real-time performance to a classroom activity or task. The latter, in particular, poses a stumbling block to many scholars seeking to objectively measure emotions and other related measures in the classroom, in real-time. The purpose of this work is to present a protocol to experimentally study students' real-time responses to exam experiences during an authentic assessment situation. For this, a team of educational psychologists, engineers, and engineering education researchers designed an experimental protocol that retained the limits required for accurate physiological sensor measurement, best-practices of salivary collection, and an authentic testing environment. In particular, existing studies that rely on physiological sensors are conducted in experimental environments that are disconnected from educational settings (e.g., Trier Stress Test), detached in time (e.g., before or after a task), or introduce analysis error (e.g., use of sensors in environments where students are likely to move). This limits our understanding of students' real-time responses to classroom activities and tasks. Furthermore, recent research has called for more considerations to be covered around issues of recruitment, replicability, validity, setups, data cleaning, preliminary analysis, and particular circumstances (e.g., adding a variable in the experimental design) in academic emotions research that relies on multi-modal approaches.