This explorative study aims to examine if electrodermal activity (EDA) and heart rate (HR) are appropriate measures for identifying and monitoring academic emotions during learning in computer-based learning environments (CBLEs). Understanding learners’ emotions while using CBLEs, allows improving the design of CBLEs. Therefore, we collected EDA, HR, and self-report data from 32 participants to measure academic emotions during learning with CBLEs in a laboratory setting. We induced negative academic emotions during learning using harmful connotated learning content about animal welfare. In a pre-post design, participants reported their emotional state before and after learning. We collated the self-reports with the EDA and HR curves to identify the emotional change in real-time. We prepared the data for repeated measurement analyses and group differences (high-, middle-, low learning performance; bored vs. not bored participants). Negative academic emotions were detected in increased EDA and HR. EDA turned out to be an indicator of learning performance. Boredom manifested in HR decrease. Findings show that EDA and HR are appropriate tools to measure academic emotions. We want to show the importance of real-time measures for learning and the efficiency of EDA and HR measures. It is worth considering EDA as a predictor for learning success and implementing EDA and HR measurements in CBLEs. However, more research is needed to clarify the role of HR in the context of learning performance.