Since COVID-19 pandemic started, schools had to face environmental changes, one was shifting from a face-to-face educational approach to online learning. It represented an unfavourable learning environment, especially for children with Specific Learning Disabilities (SpLD). Following the Self Determination Theory (SDT) framework, the current study investigated the differences in cognitive, emotional, and motivational domains between students with SpLD and undiagnosed peers, and the relations between executive functioning, emotional distress, and academic motivation. Participants included 97 Italian students, 47 with SpLD (average age of 10.9 years, SD = 1.35), and 50 undiagnosed peers (average age of 10.7 years, SD = 1.58) attending OL lectures during COVID-19. Results displayed lower executive functions (EFs), higher levels of emotional distress in students with SpLD. Furthermore, students with SpLD showed lower levels of identified and intrinsic motivation but higher levels of introjected motivation.