This study explored student teachers' cognitive presence and learning achievements by integrating the SOP[superscript 2] Model in which self-study (S), online group discussion (O) and double-stage presentations (P[superscript 2]) were implemented in the flipped classroom. The research was conducted at a university in Taiwan with 31 student teachers. Pre- and post-worksheets measuring knowledge of educational issues were administered before and after group discussion. Quantitative content analysis and behavior sequential analysis were used to evaluate cognitive presence, while a paired-samples t-test analyzed learning achievement. The results showed that the participants had the highest proportion of "Exploration," the second largest rate of "Integration," but rarely reached "Resolution." The participants' achievements were greatly enhanced using the SOP[superscript 2] Model in terms of the scores of the pre- and post-worksheets. Moreover, the groups with a higher proportion of "Integration" (I) and "Resolution" (R) performed best in the post-worksheets and were also the most progressive groups. Both high- and low-rated groups had significant correlations between the "I" and "R" phases, with "I" [right arrow] "R" in the low-rated groups but "R" [right arrow] "I" in the high-rated groups. The instructional design of the SOP[superscript 2] Model can be a reference for future pedagogical implementations in the higher educational context.