Inquiry-based learning (IBL) in mathematics is a student-centered approach that encourages exploration, problem-solving, and critical thinking, allowing students to actively engage with mathematical concepts and discover relationships through hands-on activities and collaborative learning. Despite the growing interest in IBL within mathematics education, which has demonstrated the effectiveness of this method on students' achievements, less is known about its impact on Gagné's taxonomy of knowledge (conceptual, procedural, and problem-solving knowledge). This study, based on Bruner's instructional model, compares the effectiveness of IBL against traditional teaching methods in promoting mathematical learning across Gagné's three taxonomies of knowledge in Grade 9 algebra content, using a sample of 258 Slovenian students (132 in the experimental group). Results show that the experimental group outperformed the control group in most areas, with no significant difference observed in procedural knowledge. The study suggests that IBL enhances students' conceptual understanding and problem-solving abilities by fostering deeper engagement and critical thinking but may not have the same impact on procedural fluency, which requires repetitive practice.