The relative contribution of motivational and cognitive factors to reading comprehension might depend on how reading comprehension is measured. The participants in this study were 146 students attending grade 7. Students' reading comprehension of a history text was assessed through three measures, literal comprehension, inferential comprehension, and free recall. Students' prior knowledge, reading motivation, topic interest, inference-making skills, and metacognition were also assessed. According to the multivariate general linear model, the set of motivational and cognitive variables explained students' performance in inferential comprehension and free recall, but not in literal comprehension. Moreover, topic interest moderated the association between inference-making skills and free recall. Results underlined the importance of the interplay between motivational and cognitive factors in contributing to students' deep processing of the text, but also emphasised that reading measures might not tap the same array of processes. While literal comprehension happens without the direct involvement of the cognitive-motivational variables measured in this study, believing in one own's ability in reading was associated to deep processing of the text, and free recall required the involvement of both, cognitive and motivational variables.