This study aimed to investigate the impact of yoga-based instructional design on students’ cognitive performance in attention, concentration, and memory. From a methodological standpoint, the research is applied in purpose and exploratory mixed-method in design. The first phase involved qualitative instructional design, followed by a quasi-experimental approach in the second phase. The research population consisted of elementary school students in Amol city during the academic year 1402 (2023–2024). A sample of 30 students was selected through multistage cluster sampling and randomly assigned to experimental and control groups. The data collection instruments included: The D2 Attention Test, The Cambridge Neuropsychological Test Automated Battery (CANTAB) and The Verbal Recognition Memory (VRM) Test. Data analysis was conducted using ANCOVA (Analysis of Covariance) to examine the effect of yoga-based instructional design on students’ attention, concentration, and memory. The findings revealed a statistically significant difference (p < 0.05) between the post-test scores of the experimental and control groups, after controlling for pre-test differences in the targeted cognitive domains. Therefore, the yoga-integrated instructional design demonstrated a meaningful positive effect on enhancing students’ attention, concentration, and memory performance.