In the context of inquiry-based learning, it is widely acknowledged that fostering teachers' skills in formative assessment is vital for enhancing student learning. This study examined the impact of a formative assessment-based inquiry model on science student understanding and explanations. A quasi-experimental approach that adopts the design of two groups was used. The study sample included 62 science students enrolled in the 10th grade in Saudi Arabia who were randomly assigned to an experimental group (n = 31) or a control group (n = 31). The experimental group was taught by teachers who were engaged in professional development that embedded formative assessment into teaching 5Es inquiry learning while the control group was taught conventionally. Pre- and posttests that consisted of two sections: multiple-choice (20 questions with four alternative answers) and five open-ended questions were given to the two groups. Independent sample t-tests were performed to assess the students’ understanding and explanations of physical and chemical changes. Posttest results show that students in the experimental group significantly outperformed their peers in the control group in the multiple choice and the open-ended questions. The study findings suggest the significance of integrating formative assessment with inquiry-based learning to support teachers in exploring prior knowledge and promoting learners' diverse responses. Further research should study factors that impact teachers' actions to challenge learners' thinking and encourage their inquiry to address their inconsistent views and explanations.