The number of surgical procedures requiring bone grafts is constantly increasing every year. Current grafting strategies have drawbacks such as donor site morbidity, limited availability, high costs, limited efficiency and the transmission of pathogens. Tissue engineering can offer an alternative to current treatments with the production of engineered bone grafts combining biomaterials, stem cells and osteoinductive signals. To date, no single technique exists, that can independently evaluate the quality of mesenchymal stem cell (MSC) osteogenic differentiation in a specific and sensitive manner. Instead, low sensitivity, low specificity and expensive techniques have to be combined often with conflicting results. Evidence shows that MSC metabolism changes during osteogenic differentiation and such changes can be comprehensively examined with the use of metabolomics. Therefore, given the fact that metabolism dynamically receives and responds to both genetic and environmental signals and reflects the cellular phenotype, the application of metabolomics has been assessed as a robust and sensitive technique to evaluate osteogenic differentiaton. This thesis has utilised umbilical cord derived MSCs which are a promising stem cell source for tissue engineering purposes. Metabolomics have been used to study the physiology of undifferentiated MSCs and comprehensively examine MSC metabolic physiology during 2D osteogenic differentiation with two different osteoinductive agents. The results presented herein showed that metabolism of cells differentiated with the most potent agent, closely resembled metabolism of primary osteoblasts. Subsequently, metabolomics was sensitive enough to successfully evaluate the efficiency of novel RGD-functionalised 3D scaffolds to induce osteogenic differentiation. Finally, novel alginate hydrogels have been developed with the glycyl-L-histidyl-L-lysine peptide (GHK) peptide, showing that metabolomics can provide important information during biomaterial development, by indicating the efficiency of GHK hydrogels to promote osteogenesis, assessing the reproducibility of cellular phenotype and assisting in the delineation of mechanisms underlying the function of GHK.