Notwithstanding the advantages of incorporating Augmented Reality (AR) in education, AR's concrete uses as compared to other technologies are not fully recognised. Moreover, many of the existing studies have neglected to examine the impact of pedagogy and its corresponding instructional models, whilst implementing AR in teaching and learning. In leveraging the affordances of AR, an inquiry-based learning framework, referred to as QIMS, was proposed in this study. A learning package was developed on the topic of plant reproduction for primary 5 students (aged 11-12) based on the QIMS framework. Using a quasi-experimental approach, this study evaluated three conditions (AR and QIMS; QIMS; Non-AR and Non-QIMS) for a series of science lessons in a primary school. 117 students took part in this study. The quantitative results showed that although there was no statistically significant difference in students' academic performance when AR was used, students' self-directed learning and creative thinking skills increased significantly after partaking in the QIMS inquiry-based lessons. The usage of AR and QIMS had a significant effect in increasing students' critical thinking and knowledge creation efficacy skills. Moreover, in view of students' academic outcomes, the integration of QIMS and AR proved to be more beneficial to low-progress students. Qualitative analysis of the interview data from teachers and students aids in accounting for the quantitative results and indicate productive implementation strategies. The findings of this study will guide the design of future AR interventions, by providing insights for both researchers and practitioners on how to integrate and implement AR with pedagogical approaches.