Background: The match between students' perceptions of a learning environment and their preferences about its design influences students' learning behaviour and by consequence the effectiveness of education. Therefore, the students' perspective deserves a more prominent place in the educational design process. Having an adequate picture of the match between students' perceptions and preferences is needed for teachers/educational designers to account for students' perspectives while designing education. As perception–preference match is likely to differ between students, establishing correlates to it would provide valuable information. Students' perceptions are known to relate to several student characteristics; this study extends our understanding to its relations with perception–preference match. Purpose: This study aims to investigate the degree to which students' perceptions of lessons match with their preferences about different characteristics of modern education. Additionally, it is aimed to determine the most prominent relationships between perception–preference match and learning-related student characteristics. Sample: The sample consisted of 1146 10th-grade high school students (mean age = 16 years) from five secondary schools in the Netherlands. As data collection took place during normal school hours, the response rate was 100%, comprising all students that were at school on the day of data collection. Design and methods: To measure students' perceptions of the lessons and their preferences about its instructional design, students completed the Inventory of Perceived Study Environment Extended, being composed of eight scales about central characteristics of modern education. The Inventory of Learning Styles was administered to measure learning-related student characteristics: cognitive processing strategies, regulation strategies, motivational orientations, conceptions about learning and affective processing strategies. To answer the research questions, paired t-tests and multiple regression analyses were conducted. Results: Findings showed low perception–preference matches on fascinating contents, clarity of goals and student autonomy. Students preferred these characteristics being more represented in their lessons than they actually perceived them. Perception–preference match was predominantly related to students' motivation and affective state: a personally interested motivational orientation related to better perception–preference match, whereas motivation/concentration problems related to worse matches. These relations did not give indications about causality, but based on the literature a bidirectional relation is supposed. Conclusion: This study shows that students' perception–preference match gives clear indications for which aspects of lessons could be improved. As students consider almost all characteristics of modern education as desirable, meeting students' preferences could contribute to more effective education. Additionally, the perception–preference match relates to students' motivation and affective strategies. Improving education by accounting for the match between students' perceptions and preferences of education is likely to improve motivation as well as having a significant effect on the quality of education.