Colloidal assembly of silica (nano)particles is a powerful method to design functional materials across multiple length scales. Although this method has enabled the fabrication of a wide range of silica‐based materials, attempts to design and synthesize porous materials with a high level of tuneability and control over pore dimensions have remained relatively unsuccessful. Here, the colloidal assembly of silica nanoparticles into mesoporous silica microspheres (MSMs) is reported using a discrete set of silica sols within the confinement of a water‐in‐oil emulsion system. By studying the independent manipulation of different assembly parameters during the sol–gel process, a design strategy is outlined to synthesize MSMs with excellent reproducibility and independent control over pore size and overall porosity, which does not require additional ageing or post‐treatment steps to reach pore sizes as large as 50 nm. The strategy presented here can provide the necessary tools for the microstructural design of the next generation of tailor‐made silica microspheres for use in separation applications and beyond.