This study aimed to compare the impact of e-portfolios on the motivation and autonomy of English as a Foreign Language (EFL) learners. Ninety intermediate learners were selected from 120 volunteers at a Tehran Language Institute. They were divided into three groups: two experimental groups using eportfolios and the other using paper-based portfolios, and a control group. Pre-intervention autonomy and motivation were measured using the Motivated Strategies for Learning Questionnaire (MSLQ) and Learner Autonomy Questionnaire (LAQ). A 42-session intervention involving e-portfolios, paper-based portfolios, and standard assessment methods was conducted. The results showed a positive impact of e-portfolios, including self- and peer-assessment, on learners' motivation and autonomy, while paper-based portfolio annotations also yielded positive results. These findings are valuable for researchers, educators, and learners in the language education sector.