<p>Systematic analyses of repeated measures of cognitive load during realistic, complex learning tasks are still lacking. Previous findings are based on simulations and the use of a set of multiple short problem-solving tasks. For the present study, lower secondary level pupils (<i>N</i>&#xa0;=&#xa0;360) worked on three worked examples on the topic of acids in their chemistry lessons. Cognitive load (invested mental effort and perceived task difficulty), interest, and self-assessed understanding were measured at seven points during the completion of each example. The study examines differences between repeated measures of cognitive load and interest and the relationship between the variables. The results show that the values of the repeated measures differ significantly and are poorly represented by the mean value across the measurement points. In addition, the pairwise relationship between the variables (invested effort, perceived task difficulty, interest, and self-assessed understanding) is not constant at different measurement points. Further analyses also show that different intervention conditions during the learning phase and prior knowledge are additional influencing factors.</p>