The purpose of this study was to investigate the effect of implementing a program based on integrating metacognition and habits of mind to develop secondary school students’ EFL critical reading, free writing skills and reflective thinking. The participants of the study consisted of seventy female EFL students from first year secondary students at Al Horreya secondary school for girls. The mixed design was adopted and the participants were divided in to two groups: an experimental group (n=35) and a control group (n=35). To achieve the purpose of the study, the researcher designed the study instruments: (1) An EFL critical reading skills test, (2) An EFL free writing skills test and (3) A reflective thinking questionnaire. Then a program based on integrating metacognition and habits of mind was designed and administered to the experimental group whereas the control group received regular instruction. The study instruments were pre- and post-administered to both the experimental and control group participants. Results of the study indicated that the experimental group outperformed the control group in their EFL critical reading, EFL free writing and reflective thinking. Findings of the current study provided evidence that integrating metacognition and habits of mind had a positive and significant effect on developing EFL critical reading, EFL free writing skills and reflective thinking of the experimental group. Finally, some recommendations and suggestions for further research were provided.