The rapid growth of least-material-wasting manufacturing technology, mainly called additive manufacturing (AM), has revolutionized modern fabrication industries. One of the keen features of this technology is mimicking natural materials along with the structures at micro- and nano-levels. This also enables the synthesis of various materials having nature-inspired functionalities and compositions that includes numerous bio-inspired ceramics, glasses, polymers, composites, and functionally graded materials for bone scaffolds. Thus, material selection for fabricating such bones becomes challenging among these options. The study suggests prioritizing biocompatibility-based properties and using a hybrid multi-criteria decision-making (MCDM) technique to select appropriate materials for bone scaffolds with low-load applications. Twenty properties were gathered for the ranking of six polymer and ceramic-based composites as alternatives. The hybrid MCDM integrates the stepwise weight assessment ratio analysis (SWARA) method for analyzing the weights of each property, and the complex proportional assessment (COPRAS) method was used to select the best alternative. As the biocompatibility-based properties were prioritized during selection, the natural polymer-based composites were found to have better ranks than the synthetic polymer-based composites. The best alternative was identified as the Chitosan-HA composite. The present study will help researchers and medical experts choose the best material to construct the necessary bone structure and will turn disagreements into an opportunity to give weight to the factors that were considered before making a decision.