Recent research indicates the significant potential of artificial intelligence (AI) in enhancing teachers’ instructional practices in areas such as lesson planning, personalized teacher intervention and feedback, and performance assessment. To fully realize the potential of AI in teaching, it is crucial to understand how teachers innovatively apply and critically evaluate AI applications in their teaching practices. However, there is a research gap in investigating how teachers use various features of an AI-enabled system and their perceptions of AI integration in teaching to promote teachers’ effective AI integration practices. Employing an exploratory case study design, we investigated how six science teachers utilized an AI-enabled inquiry intelligent tutoring system (Inq-ITS) within their teaching and examined their perceptions of AI integration. Classroom observations and teacher interview data were collected. When using Inq-ITS functionalities, two teachers with a pedagogical orientation of teacher-guided scientific inquiry mainly engaged with its virtual tutor and teacher report summary features. Conversely, four teachers, practicing the pedagogical orientation of AI-guided scientific inquiry, relied on the AI system to guide student learning, interacting intensively with its features, particularly real-time teacher alerts and teacher inquiry practice support. Regardless of the differences in using Inq-ITS features, all teachers recognized the potential benefits of pedagogical change and encountered various challenges. This analysis also revealed that teachers exhibited distinct perceptions regarding the role of Inq-ITS integration in their teaching. Teachers who adopted a teacher-guided pedagogical orientation perceived the Inq-ITS as a supporting tool that enhanced traditional teaching methods. In contrast, those with an AI-guided pedagogical orientation viewed the Inq-ITS as akin to a teaching assistant and a pedagogical collaborator. The findings underscored the importance of enhancing teachers’ realization of the pedagogical affordance of AI in teaching through their use of AI functionalities. It is essential to consider teachers’ diverse perceptions of AI integration when promoting their integration of AI into teaching practices.