Learning Cell Biology is challenging for both sighted and visually impaired students due to its abstract nature and reliance on bidimensional depictions in textbooks, which often fail to capture the biological complexity of cell structures and functions. To implement inclusive learning environments and address the shortage of learning materials for both sighted and visually impaired students, this work aimed to design, apply, and evaluate learning tools based on digital technologies, using the principles of Educational Design Research. 3D models representing cell membranes were created and embedded in an online virtual reality (VR) environment equipped with audio descriptions and an innovative color-changing interface. Models were also optimized for embedding in an augmented reality (AR) environment on social media. Notably, our work is the first to create such an extensive library of both animate and static VR and AR-based material, covering the structural composition of the membrane, transport mechanisms, and detailed representations of membrane specializations. Additionally, we provided, in an unprecedented way, a systematic description of our results to serve as a roadmap for easy replication and adaptation within the educational community, fostering the creation of new learning tools and approaches. Evaluation of learning tools was conducted with sighted and visually impaired students from biological and health-related undergraduate courses, as well as experienced and early-career Cell Biology teachers. Data revealed positive attitudes toward visual presentation, ease of use, content quality, and effectiveness, underscoring the potential of VR and AR to improve inclusive Cell Biology learning for undergraduate audiences.