A generalized in situ synthesis approach has been developed to prepare primary‐amine‐terminated mesoporous silica particles incorporated with a wide range of nanoparticles in the size range 2–50 nm, such as quantum dots, iron oxide nanoparticles, doped semiconductor nanocrystals, and gold nanorods. The resultant mesoporous particles are 50–800 nm in size and have a primary‐amine‐terminated surface and different morphology such as isolated spheres, rods, wires, or covalently connected aggregates. These mesoporous particles can be transformed into different functional nanoparticles for diverse applications such as drug delivery, bioimaging, and water purification. Quantum dot incorporated mesoporous particles have been demonstrated as multifunctional drug delivery carriers with simultaneous use as imaging probes. Similarly, quantum dot/gold nanorod incorporated mesoporous particles have been used as cellular imaging probes and their cellular interaction/uptake have been enhanced after functionalization with oleyl or TAT peptide.