Evolution is one of the most conceptually challenging and socially contested topics in secondary biology education. Many students enter the classroom with persistent misconceptions and naïve epistemic beliefs that hinder their ability to understand evolutionary concepts scientifically. These difficulties are often reinforced by cultural, religious, and sociocultural influences that shape learners’ attitudes toward evolution. This study investigated the impact of Guided Inquiry Based Learning (GIBL) on Grade 12 students’ learning achievement, conceptual understanding, and epistemic beliefs regarding evolution at Fasilo Secondary and Preparatory School in Bahir Dar, Ethiopia. The study employed a mixed methods approach within a Design Based Research (DBR) framework and involved 55 students from one intact classroom. Initial classroom observations, diagnostic assessments, and student discussions were conducted to identify learning difficulties and misconceptions that informed the design and refinement of the intervention. Throughout implementation, formative evidence gathered from classroom activities and student responses was used to iteratively refine inquiry tasks and instructional scaffolds in accordance with DBR principles. Data were collected using pre tests and post tests, two tier conceptual understanding tests, epistemic belief questionnaires, classroom observations, and qualitative student reflections. The quantitative findings revealed significant improvements in students’ learning achievement, with mean scores increasing from 9.16 (SD = 2.84) to 13.60 (SD = 2.95). Likewise, students’ conceptual understanding improved substantially, with mean scores increasing from 3.85 to 7.56 and a normalized gain score of 0.60, indicating a medium conceptual gain. Item level Wilcoxon Signed Rank analyses further revealed significant improvements across all five targeted misconception domains (p < .001), while the proportion of students exhibiting misconceptions decreased from 40.7% before the intervention to 9.8% afterward. Furthermore, students demonstrated significant improvement in their epistemic beliefs, with mean scores increasing from 26.96 to 32.29, t(54) = 4.26, p < .001, and a moderate effect size (d = 0.57). The intervention produced a large effect on learning achievement (Cohen’s d = 1.16) and conceptual understanding (Cohen’s d = 1.42), while a moderate effect was observed for epistemic beliefs (Cohen’s d xi = 0.57). Qualitative findings corroborated these results by revealing improved scientific reasoning, greater engagement in inquiry activities, and an enhanced ability to distinguish scientific explanations from personal beliefs. Overall, the findings indicate that Guided Inquiry--Based Learning is an effective instructional approach for improving students’ achievement, promoting conceptual change, reducing misconceptions, and fostering more sophisticated epistemic beliefs about evolution.