MiRNA-based therapies represent an innovative and promising strategy applicable to various medical fields, such as tissue regeneration and the treatment of numerous diseases, including cancer, cardiovascular problems, and viral infections. MiRNAs, a group of small non-coding RNAs, play a critical role in regulating gene expression at the post-transcriptional level and modulate several signaling pathways that maintain cellular and tissue homeostasis. The clinical trials discussed in the review herald a new therapeutic era for miRNAs, particularly in tissue engineering, using synthetic exogenous mimic miRNAs and antisense miRNAs (anti-miRNAs) to restore tissue health. This review provides an overview of miRNAs’ biogenesis, mechanism of action, regulation, and potential applications, followed by an examination of the challenges associated with the transport and delivery of therapeutic miRNAs. The possibility of using viral and non-viral vectors that protect against degradation and ensure effective miRNA delivery is highlighted, focusing on the advantages of the emerging use of 3D biomaterial scaffolds for the delivery of mimic miRNAs and anti-miRNAs to facilitate tissue repair and regeneration. Finally, the review assesses the current landscape of miRNA-activated scaffold therapies on preclinical and clinical studies in bone, cartilage, and skin tissues, emphasizing their emergence as a promising frontier in personalized medicine.