This study using a mixed methods design investigated the effects of strategy-based instruction (SBI) in a writing course on enhancing self-regulated learning and writing performance. In so doing, in the quantitative phase, employing a randomized control trial design, Iranian EFL learners in two province were first randomly assigned to classes and then classes were randomly assigned to an experimental or control condition. The total number of classes randomized was 47, with 26 experimental and 21 control. A sixteen-week metacognition training program was integrated into the writing course of the experimental groups. The students in the control groups received the regular writing program. Findings obtained from the randomized control trial design indicated significant differences in favor of the experimental students on the self-regulated learning and writing performance. To reveal a more comprehensive understanding of the SBI’s effect, in the qualitative phase, semi-structured interviews investigating student perception of the SBI program in writing course were conducted with a purposefully selected subgroup of participants. Overall, this study provides strong empirical evidence in favor of SBI in enhancing learner’s self-regulation and their writing ability.