Designing educational materials for digital resources that accommodate different learning styles and educational backgrounds is challenging due to the complexity of student engagement with content. This study examined the impact of E-learning instructional designs on students’ knowledge gain, focusing on learning approaches and perceived usefulness. The 'Virtual Histology Lab.’ (VHL), a self-learning E-resource, was developed to deliver theoretical knowledge on microscope slide preparation, incorporating cognitive scaffolding strategies such as contextualized trigger questions, map-based visualizations, and multimedia elements grounded in sound pedagogical principles. Fifty-one students with no prior exposure to slide preparation participated in the study. Knowledge gain was assessed through pre-test and post-test scenarios, while three questionnaires evaluated learning approaches, perceived usefulness, ease of use, and student perspectives on the VHL’s content. The findings revealed that 78% of students predominantly adopted a deep learning approach, while a smaller proportion exhibited a surface approach. No significant differences were observed between the pre-test and post-test scores of students with deep or surface learning approaches. However, all students demonstrated a statistically significant increase in post-test scores, indicating substantial knowledge gains across diverse learning styles. This study shares instructional design strategies to accommodate different learning styles, increase knowledge gain, and promote meaningful learning experiences.