This study has considered the integration of genre-based instruction and multimodality into two academic writing courses among 34 EFL graduate and undergraduate students in Taiwan. Analysis of the self- and peer evaluations, interviews, and multimodal writing portfolios reached the following conclusions. First, participants in this study had a positive attitude toward multimodal writing portfolios and their knowledge on academic writing particularly improved in relation to the structure of academic papers and the APA format in the post-test. Moreover, the multimodal writing portfolios enabled participants to keep a record of their writing and prepared participants to become competent researchers. Finally, participants regarded the class PowerPoint slides, the instructor’s modeling, and writing tasks as beneficial to their academic writing. The framework and suggestions on course designs for academic writing can inform educators on the integration of multimodality in academic discourse.