In this study we explored whether physiological measurement technologies could be used in a combination with traditional educational research methods to investigate learning experiences. We aimed, first, to explore individual physiological reactions during learning and how these reactions relate to experiences, emotions and contexts of learning and, second, to test new methodology and its suitability for investigating learning. The data was collected during a teacher education programme in a Finnish university. A total of 14 students participated in the study. The data was collected during two contact periods of three days and the weekends after them, ten days in total. We used a mixed method approach and collected various kind of data: quantitative heart rate variability data, qualitative diaries, videos, interviews and questionnaires. Heart rate variability data was analyzed by using SPSS, interviews were transcribed, and a content analysis was performed. Meaningful learning episodes and experiences reported by the students were linked to the physiological data. In addition to the heart rate variability analysis on sequential learning related activities, the heart rate variability between different days and periods was also conducted. Overall heart rate variability varied between days and showed recovery during weekends. The daily differences in physiological alertness (derived from heart rate variability analysis) corresponded to the student reports, suggesting that small group work facilitated by the teacher was physiologically more alerting/engaging and also experienced as more meaningful than the lectures. In addition, comparisons between sequential activities with similar learning situations but with different contents showed differences in alertness. This may be due to subtle changes in the composition of the activities or students’ physiological state. Exploring learning in natural contexts involves challenges, such as various uncontrolled variables in people's lives. Therefore, further studies with larger samples, different contexts and meaningful episodes related more detail analyses are needed.