The objective of this study was to investigate the effect of inquiry-based learning (IBL) on EFL learners’ WTC and speaking skills in L2 online flipped classrooms. IBL involves learners in question-answer interactive information exchanges and participating actively in cognitive and discovery learning activities. The inquiry-based flipped approach employed in this study required two groups of intermediate Iranian EFL learners to study some online materials provided through telegram. The groups were assigned to structured-inquiry flipped learning and open-inquiry flipped learning conditions, varied from an information-framing mode to a fully discovery-oriented one with the same instructor. In the pre-class phase, the learners watched the videos and listened to the audio docs related to the topic of every classroom discussion. The students’ WTC and speaking performance were analysed both prior to and after the experiment. The quantitative data analysis indicated that the open-inquiry flipped approach significantly improved students’ WTC and speaking skills. Qualitative data analysis showed that the proposed approach enhanced the learners’ WTC and speaking skills by fostering motivation and reducing state anxiety. The findings of the study provide guidance for flipped practitioners to develop effective teaching designs for conducting flipped-based learning activities.