As learners are working individually in e-learning environments, research has moved to focus on providing guidance for learners and helping them to take responsibility for their own learning. Therefore, this study aimed to shed light on both learner autonomy and scaffolding in e-learning environments. 35 international English as a Foreign Language (EFL) students who were taking a course supported with online learning resources (OLRs) including the English for Academic Purposes (EAP) Toolkit participated in the study voluntarily. Before taking the course, they filled a pre-questionnaire about their perceptions of learning, whilst a post-questionnaire at the end of the course. In the meantime, they were observed three times while carrying out activities in the Toolkit, and interviewed afterwards. Data from observations, interviews and questionnaires have shown that e-learning through scaffolding facilitates EFL learners' language learning and scaffolding has a significant impact on learner autonomy and vice versa. This study sets the grounds for learners to use scaffolding, teachers to implement scaffolding, institutions to provide a scaffolded autonomous e-learning environment and designers to set up that kind of environment in order to enable the educational equality and opportunity for all learners.