This study examined the relationship between students’ subjective experiences and their perceived sense of challenge, threat, motivation, and self-efficacy in virtual and blended learning environments. Utilizing a mixed-methods approach, data were collected from 484 students across two academic institutions in Israel. The findings revealed significant associations between students’ emotional perceptions and their levels of engagement, persistence, and satisfaction with the learning process. Notable differences emerged across academic disciplines and year of study. Blended learning environments foster richer interpersonal interaction, whereas virtual platforms promote higher-order thinking and multimedia engagement, while also presenting distinct emotional and communicative challenges. The study underscores the critical importance of accounting for students’ affective responses when designing and implementing effective digital learning experiences.