While recognizing the vital role of teachers in augmented reality (AR) integration, a noticeable literature gap exists regarding how science educators address challenges related to technology, pedagogy, and content during AR instructional design and implementation. Conducted in a secondary school in Taiwan, this study addressed this gap by conducting a qualitative single-case analysis of a science teacher’s integration of AR technology into her biology lessons. The teacher’s pedagogical reasoning and action processes were observed and analyzed over 10 weeks, with a focus on micro-level exploration across two iterations of pedagogical analysis, design, implementation, reflection, and revision. The primary data collection includes teacher interviews, supplemented by teacher reflective notes, lesson plans, teaching materials, researcher observations and field notes taken during the weekly, one-hour teacher learning community meetings, and the AR-integrated lessons, student assessment results, and feedback. The study was informed by both the Technology Integration Planning model and the Technological Pedagogical Content Knowledge framework. Data analysis techniques involved deductive coding and thematic analysis. The findings reveal the teacher’s developmental proficiency in AR, a reimagined depiction of AR-enhanced instructional content, a shift from didactic-based to inquiry-based teaching approaches, and an intertwined development of technological pedagogical knowledge, technological content knowledge, and pedagogical content knowledge. This study provides valuable insights into how the educator became a pedagogical designer, overcame individual and contextual challenges, and leveraged reflective strategies to enhance biology lessons using AR technology, emphasizing technology’s potential to enrich pedagogy in science education.