Inspired by the complex diversity of collagenous materials in mammalian tissue, collagen-based biomaterials are increasingly utilized for developing drug delivery vehicles and regenerative tissue engineering. Collagen's broad utility poses important engineering challenges for the rational and predictive design of the resultant biomaterial's physical and chemical properties. We review the most recent developments in multiscale computational modeling of collagen-based biomaterials to determine their structural, mechanical, and physicochemical properties. Through the materials-by-design paradigm, these developments may eventually lead to rational algorithmic recipes for bottom–up multiscale design of these biomaterials, thereby minimizing the experimental costs of iterative material synthesis and testing. We also highlight the future perspectives and opportunities for expanding multiscale modeling capabilities to incorporate physicochemical and biological functions of collagen-based biomaterials.