We present three studies pertaining to learning, engagement and motivation during laboratory lessons in three high school biology classrooms. In the first, quantitative methods are used to compare students’ in-the-moment reports of learning, engagement, and motivation during laboratory with other classroom activities. Data were collected with the Experience Sampling Method (ESM). Students reported equivalent learning, less engagement, lower relevance and more enjoyment and interest during lab than during other activities. In the second study, video data from one laboratory lesson pertaining to pH in those classes was coded using event sampling and discourse analysis in an effort to understand the students’ reports. A scientist with expertise in the lab topic also watched the videos while thinking aloud. Results showed that the lab was limited in terms of practices promoting learning, engagement and relevance. Finally, responses from an interview with each teacher and the scientist about the goals and relevance of the laboratory for students were analyzed to shed further light on the findings from the first two studies. Results are discussed in terms of how laboratory lessons might be improved to enhance student learning, engagement, and motivation.