The idea of multifunctional nanomedicine that enters the human body to diagnose and treat disease without major surgery is a long-standing dream of nanomaterials scientists. Nanomaterials show incredible properties that are not found in bulk materials, but achieving multi-functionality on a single material remains challenging. Integrating several types of materials at the nano-scale is critical to the success of multifunctional nanomedicine device. Here, we describe the advantages of silica nanoparticles as a tool for multifunctional nano-devices. Silica nanoparticles have been intensively studied in drug delivery due to their biocompatibility, degradability, tunable morphology, and ease of modification. Moreover, silica nanoparticles can be integrated with other materials to obtain more features and achieve theranostic capabilities and multimodality for imaging applications. In this review, we will first compare the properties of silica nanoparticles with other well-known nanomaterials for bio-applications and describe typical routes to synthesize and integrate silica nanoparticles. We will then highlight theranostic and multimodal imaging application that use silica-based nanoparticles with a particular interest in real-time monitoring of therapeutic molecules. Finally, we will present the challenges and perspective on future work with silica-based nanoparticles in medicine.