Metabolic Syndrome and bone diseases are high priority human diseases which, scientists have tried to better understand in order to aid those suffering from their detrimental effects. Therapies for Metabolic Syndrome and bone diseases available today come with several side effects and do not alleviate the conditions fully; thus, it is beneficial to find alternative medicines and treatments which have the potential to provide less or optimal side effects. Salvia hispanica is a medicinal and edible plant known for its high nutritional value and therapeutically potential which shows promise in possessing properties useful in developing alternative therapies or treatments for metabolic syndrome and bone diseases. miRNA expression patterns can be disease-specific, reflect the developmental and state of tumors or cancers but equally important they are essential biological processes which, may lead to various pathological and occasionally malignant outcomes. Mouse MC3TC cells were cultured, differentiated, and treated with aqueous extract of the seeds of S. hispanica for 48 hours. The cells were then harvested and sent for miRNA analysis. The data revealed that the S. hispanica seed extract up-regulated let-7e-5p, let-7a-5p, let-7j, and miRNA-151-5p. Moreover, the data revealed that several miRNAs were downregulated including miRNA-181a-5p, miRNA-503-5p, miRNA106b-5p, miRNA-152-5p, miRNA-140-3p, miRNA-33-5p, miRNA-214-3p, miRNA-99b-5p, miRNA-30c-2-3p, miRNA199a-5p. The knowledge extrapolated regarding the miRNAs and the metabolic pathways that are impacted by Salvia hispanica will help us identify the benefits of S. hispanica in treating Metabolic Syndrome and bone diseases.