Mesoporous silica nanoparticles (MSNs) are a key example of the innovation in material science to develop nanotechnology-based delivery systems. Biological and pharmaceutical applications of the MSNs garnered more attention recently due to their potential in carrying therapeutic agents. When utilized as nanocarriers, the uniquely structured MSNs are capable of acting as an effective drug, gene, protein, and antigen delivery vehicle for an assortment of therapeutic regimens to mitigate the progress of diseases, inflammatory responses, and cancer. The biocompatibility of MSN particles along with their multipurpose applications have been the subject of multiple studies in the nano/biotechnology and nanomedical communities concerning the effective and safe use of these delivery systems for diagnosis and management of various diseases. Concentrating on their drug vector applicability, this review presents an in-depth overview and discussion on the biosafety of MSNs and their evaluation in clinical trials. Additionally, other impactful issues surrounding the synthetic aspects, biological use (i.e., drug delivery, gene delivery, protein delivery and antigen delivery), uptake pathway, as well as other points of interest for MSNs will be discussed. To conclude the review, a discussion concerning emerging trends alongside the anticipated future advancements for these carries will be undertaken.